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Title: Analysis essentials — Analysis essentials documentation

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Domain: hsf-training.github.io

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Analysis essentials https://hsf-training.github.io/analysis-essentials/
An introduction to Pythonhttps://hsf-training.github.io/analysis-essentials/python/README.html
Running Pythonhttps://hsf-training.github.io/analysis-essentials/python/running.html
Scriptinghttps://hsf-training.github.io/analysis-essentials/python/00scripts.html
argparsehttps://hsf-training.github.io/analysis-essentials/python/00scripts.html#argparse
1: Basicshttps://hsf-training.github.io/analysis-essentials/python/01basics.html
Jupyterhttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Jupyter
Basic types and operationshttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Basic-types-and-operations
strong typinghttps://hsf-training.github.io/analysis-essentials/python/01basics.html#strong-typing
Container typeshttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Container-types
Mutabilityhttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Mutability
dynamic typinghttps://hsf-training.github.io/analysis-essentials/python/01basics.html#dynamic-typing
Assignement and variableshttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Assignement-and-variables
Python variable assignementhttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Python-variable-assignement
Sugar: comprehensionshttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Sugar:-comprehensions
Sugar: using Markdownhttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Sugar:-using-Markdown
Objects and operatorshttps://hsf-training.github.io/analysis-essentials/python/operators.html
Objectshttps://hsf-training.github.io/analysis-essentials/python/operators.html#objects
Numbershttps://hsf-training.github.io/analysis-essentials/python/numbers.html
Stringshttps://hsf-training.github.io/analysis-essentials/python/strings.html
Formattinghttps://hsf-training.github.io/analysis-essentials/python/strings.html#Formatting
Lists and loopinghttps://hsf-training.github.io/analysis-essentials/python/lists.html
Loopinghttps://hsf-training.github.io/analysis-essentials/python/lists.html#Looping
Indentationhttps://hsf-training.github.io/analysis-essentials/python/lists.html#Indentation
List comprehension (Sugar, can be skipped on first read)https://hsf-training.github.io/analysis-essentials/python/lists.html#List-comprehension-(Sugar,-can-be-skipped-on-first-read)
Tupleshttps://hsf-training.github.io/analysis-essentials/python/lists.html#Tuples
Dictionarieshttps://hsf-training.github.io/analysis-essentials/python/dictionaries.html
Dictionary keyshttps://hsf-training.github.io/analysis-essentials/python/dictionaries.html#Dictionary-keys
Conditionshttps://hsf-training.github.io/analysis-essentials/python/conditions.html
Truthinesshttps://hsf-training.github.io/analysis-essentials/python/conditions.html#Truthiness
Conditions in loopshttps://hsf-training.github.io/analysis-essentials/python/conditions.html#Conditions-in-loops
Functionshttps://hsf-training.github.io/analysis-essentials/python/methods.html
*args and **kwargshttps://hsf-training.github.io/analysis-essentials/python/methods.html#*args-and-**kwargs
Inline methodshttps://hsf-training.github.io/analysis-essentials/python/methods.html#Inline-methods
Scriptinghttps://hsf-training.github.io/analysis-essentials/python/scripting.html
argparsehttps://hsf-training.github.io/analysis-essentials/python/scripting.html#argparse
Moduleshttps://hsf-training.github.io/analysis-essentials/python/modules.html
Using modules into your code: importhttps://hsf-training.github.io/analysis-essentials/python/modules.html#Using-modules-into-your-code:-import
The standard libraryhttps://hsf-training.github.io/analysis-essentials/python/modules.html#The-standard-library
Modules from PyPihttps://hsf-training.github.io/analysis-essentials/python/modules.html#Modules-from-PyPi
(Advanced) Write your first Python modulehttps://hsf-training.github.io/analysis-essentials/python/modules.html#(Advanced)-Write-your-first-Python-module
Module name restrictionshttps://hsf-training.github.io/analysis-essentials/python/modules.html#Module-name-restrictions
Write a structured modulehttps://hsf-training.github.io/analysis-essentials/python/modules.html#Write-a-structured-module
Run a modulehttps://hsf-training.github.io/analysis-essentials/python/modules.html#Run-a-module
Classeshttps://hsf-training.github.io/analysis-essentials/python/classes.html
Welcome to classeshttps://hsf-training.github.io/analysis-essentials/python/classes.html#Welcome-to-classes
Inheritance: a glancehttps://hsf-training.github.io/analysis-essentials/python/classes.html#Inheritance:-a-glance
How to fixhttps://hsf-training.github.io/analysis-essentials/python/classes.html#How-to-fix
Learning morehttps://hsf-training.github.io/analysis-essentials/python/learning.html
Exploring Pythonhttps://hsf-training.github.io/analysis-essentials/python/learning.html#exploring-python
Conventional codinghttps://hsf-training.github.io/analysis-essentials/python/learning.html#conventional-coding
Making your first histogramhttps://hsf-training.github.io/analysis-essentials/python/first_histogram.html
Pandashttps://hsf-training.github.io/analysis-essentials/python/first_histogram.html#pandas
Plotting histogramshttps://hsf-training.github.io/analysis-essentials/python/first_histogram.html#plotting-histograms
Applying cutshttps://hsf-training.github.io/analysis-essentials/python/first_histogram.html#applying-cuts
More advanced topics in Pythonhttps://hsf-training.github.io/analysis-essentials/python/further_reading.html
Nice standard librarieshttps://hsf-training.github.io/analysis-essentials/python/further_reading.html#nice-standard-libraries
Nice libraries for data analysishttps://hsf-training.github.io/analysis-essentials/python/further_reading.html#nice-libraries-for-data-analysis
Python and ROOThttps://hsf-training.github.io/analysis-essentials/python/further_reading.html#python-and-root
Advanced Python Tutorialhttps://hsf-training.github.io/analysis-essentials/advanced-python/README.html
1: Basicshttps://hsf-training.github.io/analysis-essentials/advanced-python/10Basics.html
Basicshttps://hsf-training.github.io/analysis-essentials/advanced-python/10Basics.html#Basics
Markdownhttps://hsf-training.github.io/analysis-essentials/advanced-python/10Basics.html#Markdown
Jupyterhttps://hsf-training.github.io/analysis-essentials/advanced-python/10Basics.html#Jupyter
Importing moduleshttps://hsf-training.github.io/analysis-essentials/advanced-python/10Basics.html#Importing-modules
Advanced Python Conceptshttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html
Packing and unpacking of valueshttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Packing-and-unpacking-of-values
Context managerhttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Context-manager
Using yieldhttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Using-yield
Using a classhttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Using-a-class
Decorators and factorieshttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Decorators-and-factories
Decoratorhttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Decorator
Exceptionshttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Exceptions
Custom Exceptionhttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Custom-Exception
Catching exceptionshttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Catching-exceptions
pitfall “guaranteed execution”https://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#pitfall-%22guaranteed-execution%22
Exceptions as control-flowhttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Exceptions-as-control-flow
Advanced Classeshttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html
Dunderhttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html#Dunder
lenhttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html#len
strhttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html#str
Callablehttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html#Callable
Indexing (iterating)https://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html#Indexing-(iterating)
selfhttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html#self
Danger zonehttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html#Danger-zone
2: First look at datahttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html
Two plotting libraries?https://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Two-plotting-libraries?
Recap: Importing moduleshttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Recap:-Importing-modules
5. The toy datasethttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#5.-The-toy-dataset
Loading datahttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Loading-data
6. Plotting a simple histogramhttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#6.-Plotting-a-simple-histogram
Adding variableshttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Adding-variables
Using rectangular cutshttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Using-rectangular-cuts
Comparing distributionshttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Comparing-distributions
3: Multivariate Analysishttps://hsf-training.github.io/analysis-essentials/advanced-python/30Classification.html
Using a classifierhttps://hsf-training.github.io/analysis-essentials/advanced-python/30Classification.html#Using-a-classifier
TODO Add a diagram of a decision tree for the above plothttps://hsf-training.github.io/analysis-essentials/advanced-python/30Classification.html#TODO-Add-a-diagram-of-a-decision-tree-for-the-above-plot
4: Extension on Classificationhttps://hsf-training.github.io/analysis-essentials/advanced-python/31ClassificationExtension.html
Alternative implimentationshttps://hsf-training.github.io/analysis-essentials/advanced-python/31ClassificationExtension.html#Alternative-implimentations
Feature engineeringhttps://hsf-training.github.io/analysis-essentials/advanced-python/31ClassificationExtension.html#Feature-engineering
\(k\)-foldinghttps://hsf-training.github.io/analysis-essentials/advanced-python/31ClassificationExtension.html#k-folding
Turn this into a scipt using argparsehttps://hsf-training.github.io/analysis-essentials/advanced-python/31ClassificationExtension.html#Turn-this-into-a-scipt-using-argparse
5: Boosting to Uniformityhttps://hsf-training.github.io/analysis-essentials/advanced-python/32BoostingToUniformity.html
Loading datahttps://hsf-training.github.io/analysis-essentials/advanced-python/32BoostingToUniformity.html#Loading-data
Distributions in the Dalitz features for signal and backgroundhttps://hsf-training.github.io/analysis-essentials/advanced-python/32BoostingToUniformity.html#Distributions-in-the-Dalitz-features-for-signal-and-background
Preparation of train/test datasetshttps://hsf-training.github.io/analysis-essentials/advanced-python/32BoostingToUniformity.html#Preparation-of-train/test-datasets
Setting up classifiers, traininghttps://hsf-training.github.io/analysis-essentials/advanced-python/32BoostingToUniformity.html#Setting-up-classifiers,-training
Let’s look at the results of traininghttps://hsf-training.github.io/analysis-essentials/advanced-python/32BoostingToUniformity.html#Let's-look-at-the-results-of-training
ROC curves after traininghttps://hsf-training.github.io/analysis-essentials/advanced-python/32BoostingToUniformity.html#ROC-curves-after-training
6: Histogramshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html
Axeshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Axes
Regularhttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Regular
Variablehttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Variable
Axis Namehttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Axis-Name
Compatibility with mplhephttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Compatibility-with-mplhep
Plotting with histhttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Plotting-with-hist
Multiple dimensionshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Multiple-dimensions
Access Binshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Access-Bins
Getting Densityhttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Getting-Density
Projecting axeshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Projecting-axes
Accessing everything relevanthttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Accessing-everything-relevant
Multi dimensionalhttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Multi-dimensional
Arithmeticshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Arithmetics
Weightshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Weights
7: Demonstration of distribution reweightinghttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html
Downloading datahttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Downloading-data
prepare train and test sampleshttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#prepare-train-and-test-samples
Original distributionshttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Original-distributions
train part of original distributionhttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#train-part-of-original-distribution
test part for target distributionhttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#test-part-for-target-distribution
Bins-based reweighting in n dimensionshttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Bins-based-reweighting-in-n-dimensions
Gradient Boosted Reweighterhttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Gradient-Boosted-Reweighter
Comparing some simple expressions:https://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Comparing-some-simple-expressions:
GB-discriminationhttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#GB-discrimination
Great!https://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Great!
What did just happen?https://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#What-did-just-happen?
How to tunehttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#How-to-tune
Folding reweighterhttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Folding-reweighter
GB discrimination for reweighting rulehttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#GB-discrimination-for-reweighting-rule
8: Likelihood inferencehttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html
Scope of this tutorialhttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Scope-of-this-tutorial
Getting startedhttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Getting-started
Creating the modelhttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Creating-the-model
Plottinghttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Plotting
A quick plothttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#A-quick-plot
Losshttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Loss
Fixing parametershttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Fixing-parameters
9: sPlothttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html
Simple sPlot examplehttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Simple-sPlot-example
Observed distributionshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Observed-distributions
Applying sWeightshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Applying-sWeights
Comparehttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Compare
More complex casehttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#More-complex-case
Splothttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Splot
Alternative: Known probabilitieshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Alternative:-Known-probabilities
Building sPlot over masshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Building-sPlot-over-mass
Of course we don’t have labels which events are signal and which are background beforehandhttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Of-course-we-don't-have-labels-which-events-are-signal-and-which-are-background-beforehand
We have no information about real labelshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#We-have-no-information-about-real-labels
Fitting doesn’t give us information about real labelshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Fitting-doesn't-give-us-information-about-real-labels
Appying sPlothttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Appying-sPlot
Using sWeights to reconstruct initial distributionhttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Using-sWeights-to-reconstruct-initial-distribution
An important requirement of sPlothttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#An-important-requirement-of-sPlot
Derivation of sWeights (optional)https://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Derivation-of-sWeights-(optional)
Under assumption of linearity:https://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Under-assumption-of-linearity:
Minimization of variationhttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Minimization-of-variation
Uncorrelatednesshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Uncorrelatedness
Conclusionhttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Conclusion
10: Scikit-HEPhttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html
formulate - converting expressionshttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html#formulate---converting-expressions
Particlehttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html#Particle
hepunitshttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html#hepunits
Vectorhttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html#Vector
Vector propertieshttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html#Vector-properties
Introducing the Shellhttps://hsf-training.github.io/analysis-essentials/shell/README.html
Backgroundhttps://hsf-training.github.io/analysis-essentials/shell/README.html#background
The Command-Line Interfacehttps://hsf-training.github.io/analysis-essentials/shell/README.html#the-command-line-interface
The Shellhttps://hsf-training.github.io/analysis-essentials/shell/README.html#the-shell
Why bother?https://hsf-training.github.io/analysis-essentials/shell/README.html#why-bother
Nelle’s Pipeline: Starting Pointhttps://hsf-training.github.io/analysis-essentials/shell/README.html#nelle-s-pipeline-starting-point
Navigating Files and Directorieshttps://hsf-training.github.io/analysis-essentials/shell/02-filedir.html
Nelle’s Pipeline: Organizing Fileshttps://hsf-training.github.io/analysis-essentials/shell/02-filedir.html#nelle-s-pipeline-organizing-files
Working With Files and Directorieshttps://hsf-training.github.io/analysis-essentials/shell/03-create.html
Pipes and Filtershttps://hsf-training.github.io/analysis-essentials/shell/04-pipefilter.html
Nelle’s Pipeline: Checking Fileshttps://hsf-training.github.io/analysis-essentials/shell/04-pipefilter.html#nelle-s-pipeline-checking-files
Loopshttps://hsf-training.github.io/analysis-essentials/shell/05-loop.html
Shell Scriptshttps://hsf-training.github.io/analysis-essentials/shell/06-script.html
Finding Thingshttps://hsf-training.github.io/analysis-essentials/shell/07-find.html
UNIX shellhttps://hsf-training.github.io/analysis-essentials/shell-extras/README.html
Using screen to keep things runninghttps://hsf-training.github.io/analysis-essentials/shell-extras/screen.html
Advanced screen topicshttps://hsf-training.github.io/analysis-essentials/shell-extras/screen2.html
Finding lost screenshttps://hsf-training.github.io/analysis-essentials/shell-extras/screen2.html#finding-lost-screens
Using tabs in screenhttps://hsf-training.github.io/analysis-essentials/shell-extras/screen2.html#using-tabs-in-screen
Persistent screen or tmux session on lxplushttps://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html
lxplus7https://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html#lxplus7
Setting up password-less kerberos token on lxplus7https://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html#setting-up-password-less-kerberos-token-on-lxplus7
Making use of the keytab on lxplus7https://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html#making-use-of-the-keytab-on-lxplus7
Using k5reauth to automatically refresh your kerberos token on lxplus7https://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html#using-k5reauth-to-automatically-refresh-your-kerberos-token-on-lxplus7
lxplus8https://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html#lxplus8
lxplus9https://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html#lxplus9
More about the UNIX shellhttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html
Types of shellhttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#types-of-shell
Manual pageshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#manual-pages
Environment variableshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#environment-variables
Variableshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#variables
Differences among fileshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#differences-among-files
Looping over fileshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#looping-over-files
Conditionalshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#conditionals
Linking commandshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#linking-commands
Pipes and redirectionhttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#pipes-and-redirection
Bash securityhttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#bash-security
Complexityhttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#complexity
Text viewershttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#text-viewers
Text editorshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#text-editors
Disk spacehttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#disk-space
Over the Wire and Bandit wargamehttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#over-the-wire-and-bandit-wargame
Analysis automation with Snakemakehttps://hsf-training.github.io/analysis-essentials/snakemake/README.html
Documentation and environmentshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#documentation-and-environments
Workflow preservationhttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#workflow-preservation
Basic Tutorialhttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#basic-tutorial
What is a workflow?https://hsf-training.github.io/analysis-essentials/snakemake/README.html#what-is-a-workflow
Why use a workflow management system?https://hsf-training.github.io/analysis-essentials/snakemake/README.html#why-use-a-workflow-management-system
Introducing Snakemakehttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#introducing-snakemake
Re-running ruleshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#re-running-rules
Chaining ruleshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#chaining-rules
The limits of wildcardshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#the-limits-of-wildcards
Advanced Tutorialhttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#advanced-tutorial
Running scriptshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#running-scripts
Log fileshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#log-files
Config fileshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#config-files
Includeshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#includes
Githttps://hsf-training.github.io/analysis-essentials/git/README.html
Automated Version Controlhttps://hsf-training.github.io/analysis-essentials/git/01-basics.html
Setting Up Githttps://hsf-training.github.io/analysis-essentials/git/02-setup.html
Creating a Repositoryhttps://hsf-training.github.io/analysis-essentials/git/03-create.html
Tracking Changeshttps://hsf-training.github.io/analysis-essentials/git/04-changes.html
Exploring Historyhttps://hsf-training.github.io/analysis-essentials/git/05-history.html
Ignoring Thingshttps://hsf-training.github.io/analysis-essentials/git/06-ignore.html
Remotes in CERN GitLabhttps://hsf-training.github.io/analysis-essentials/git/07-gitlab.html
Sharing a repository with othershttps://hsf-training.github.io/analysis-essentials/git/08-share.html
Collaborating with Pull Requestshttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html
What is a Pull (or Merge) Requesthttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#what-is-a-pull-or-merge-request
Fork the original project repositoryhttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#fork-the-original-project-repository
Clone a remote project and its forkhttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#clone-a-remote-project-and-its-fork
Sync your local repository with remote changeshttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#sync-your-local-repository-with-remote-changes
Implement your new featurehttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#implement-your-new-feature
Push changeshttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#push-changes
Create a Pull (or Merge) Requesthttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#create-a-pull-or-merge-request
Discussing, amending, retiring a Merge Requesthttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#discussing-amending-retiring-a-merge-request
Accepting a Pull Requesthttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#accepting-a-pull-request
The social side of codinghttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#the-social-side-of-coding
Automatic testinghttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#automatic-testing
Conflictshttps://hsf-training.github.io/analysis-essentials/git/10-conflict.html
GitLab CIhttps://hsf-training.github.io/analysis-essentials/git/11-ci.html
Open Sciencehttps://hsf-training.github.io/analysis-essentials/git/12-open.html
Licensinghttps://hsf-training.github.io/analysis-essentials/git/13-licensing.html
Citationhttps://hsf-training.github.io/analysis-essentials/git/14-citation.html
Contributinghttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html
Contributor Agreementhttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html#contributor-agreement
How to Contributehttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html#how-to-contribute
What to Contributehttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html#what-to-contribute
Using GitHubhttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html#using-github
Other Resourceshttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html#other-resources
Contributor Code of Conducthttps://hsf-training.github.io/analysis-essentials/CONDUCT.html
Instructional Materialhttps://hsf-training.github.io/analysis-essentials/LICENSE.html
Softwarehttps://hsf-training.github.io/analysis-essentials/LICENSE.html#software
Analysis essentialshttps://hsf-training.github.io/analysis-essentials/
https://hsf-training.github.io/analysis-essentials/
Edit on GitHubhttps://github.com/hsf-training/analysis-essentials/blob/master/index.md
https://github.com/hsf-training/analysis-essentials/actions/workflows/build.yml/badge.svg
https://mybinder.org/v2/gh/hsf-training/analysis-essentials/master
https://hsf-training.github.io/analysis-essentials/#analysis-essentials-build-status-binder
analysis essentials websitehttps://hsf-training.github.io/analysis-essentials/
Starterkithttps://lhcb.github.io/starterkit/
contributing guidehttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html
HSF Software Training Centerhttps://hepsoftwarefoundation.org/training/curriculum.html
https://hsf-training.github.io/analysis-essentials/#prerequisites
https://hsf-training.github.io/analysis-essentials/#local
mambaforgehttps://github.com/conda-forge/miniforge#mambaforge
conda-forgehttps://conda-forge.org/
herehttps://github.com/conda-forge/miniforge#install
Jupyterhttps://jupyterlab.readthedocs.io/
herehttps://jupyterlab.readthedocs.io/en/stable/getting_started/starting.html
https://hsf-training.github.io/analysis-essentials/#binder
https://mybinder.org/v2/gh/hsf-training/analysis-essentials/master
https://hsf-training.github.io/analysis-essentials/#usage
Analysis Essentials coursehttps://hsf-training.github.io/analysis-essentials/index.html
open an issuehttps://github.com/hsf-training/analysis-essentials/issues
An introduction to Pythonhttps://hsf-training.github.io/analysis-essentials/python/README.html
Running Pythonhttps://hsf-training.github.io/analysis-essentials/python/running.html
Scriptinghttps://hsf-training.github.io/analysis-essentials/python/00scripts.html
argparsehttps://hsf-training.github.io/analysis-essentials/python/00scripts.html#argparse
1: Basicshttps://hsf-training.github.io/analysis-essentials/python/01basics.html
Jupyterhttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Jupyter
Basic types and operationshttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Basic-types-and-operations
strong typinghttps://hsf-training.github.io/analysis-essentials/python/01basics.html#strong-typing
Container typeshttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Container-types
Mutabilityhttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Mutability
dynamic typinghttps://hsf-training.github.io/analysis-essentials/python/01basics.html#dynamic-typing
Assignement and variableshttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Assignement-and-variables
Python variable assignementhttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Python-variable-assignement
Sugar: comprehensionshttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Sugar:-comprehensions
Sugar: using Markdownhttps://hsf-training.github.io/analysis-essentials/python/01basics.html#Sugar:-using-Markdown
Objects and operatorshttps://hsf-training.github.io/analysis-essentials/python/operators.html
Objectshttps://hsf-training.github.io/analysis-essentials/python/operators.html#objects
Numbershttps://hsf-training.github.io/analysis-essentials/python/numbers.html
Stringshttps://hsf-training.github.io/analysis-essentials/python/strings.html
Formattinghttps://hsf-training.github.io/analysis-essentials/python/strings.html#Formatting
Lists and loopinghttps://hsf-training.github.io/analysis-essentials/python/lists.html
Loopinghttps://hsf-training.github.io/analysis-essentials/python/lists.html#Looping
List comprehension (Sugar, can be skipped on first read)https://hsf-training.github.io/analysis-essentials/python/lists.html#List-comprehension-(Sugar,-can-be-skipped-on-first-read)
Tupleshttps://hsf-training.github.io/analysis-essentials/python/lists.html#Tuples
Dictionarieshttps://hsf-training.github.io/analysis-essentials/python/dictionaries.html
Dictionary keyshttps://hsf-training.github.io/analysis-essentials/python/dictionaries.html#Dictionary-keys
Conditionshttps://hsf-training.github.io/analysis-essentials/python/conditions.html
Truthinesshttps://hsf-training.github.io/analysis-essentials/python/conditions.html#Truthiness
Conditions in loopshttps://hsf-training.github.io/analysis-essentials/python/conditions.html#Conditions-in-loops
Functionshttps://hsf-training.github.io/analysis-essentials/python/methods.html
*args and **kwargshttps://hsf-training.github.io/analysis-essentials/python/methods.html#*args-and-**kwargs
Inline methodshttps://hsf-training.github.io/analysis-essentials/python/methods.html#Inline-methods
Scriptinghttps://hsf-training.github.io/analysis-essentials/python/scripting.html
argparsehttps://hsf-training.github.io/analysis-essentials/python/scripting.html#argparse
Moduleshttps://hsf-training.github.io/analysis-essentials/python/modules.html
Using modules into your code: importhttps://hsf-training.github.io/analysis-essentials/python/modules.html#Using-modules-into-your-code:-import
The standard libraryhttps://hsf-training.github.io/analysis-essentials/python/modules.html#The-standard-library
Modules from PyPihttps://hsf-training.github.io/analysis-essentials/python/modules.html#Modules-from-PyPi
(Advanced) Write your first Python modulehttps://hsf-training.github.io/analysis-essentials/python/modules.html#(Advanced)-Write-your-first-Python-module
Write a structured modulehttps://hsf-training.github.io/analysis-essentials/python/modules.html#Write-a-structured-module
Run a modulehttps://hsf-training.github.io/analysis-essentials/python/modules.html#Run-a-module
Classeshttps://hsf-training.github.io/analysis-essentials/python/classes.html
Welcome to classeshttps://hsf-training.github.io/analysis-essentials/python/classes.html#Welcome-to-classes
Inheritance: a glancehttps://hsf-training.github.io/analysis-essentials/python/classes.html#Inheritance:-a-glance
Learning morehttps://hsf-training.github.io/analysis-essentials/python/learning.html
Exploring Pythonhttps://hsf-training.github.io/analysis-essentials/python/learning.html#exploring-python
Conventional codinghttps://hsf-training.github.io/analysis-essentials/python/learning.html#conventional-coding
Making your first histogramhttps://hsf-training.github.io/analysis-essentials/python/first_histogram.html
Pandashttps://hsf-training.github.io/analysis-essentials/python/first_histogram.html#pandas
Plotting histogramshttps://hsf-training.github.io/analysis-essentials/python/first_histogram.html#plotting-histograms
Applying cutshttps://hsf-training.github.io/analysis-essentials/python/first_histogram.html#applying-cuts
More advanced topics in Pythonhttps://hsf-training.github.io/analysis-essentials/python/further_reading.html
Nice standard librarieshttps://hsf-training.github.io/analysis-essentials/python/further_reading.html#nice-standard-libraries
Nice libraries for data analysishttps://hsf-training.github.io/analysis-essentials/python/further_reading.html#nice-libraries-for-data-analysis
Python and ROOThttps://hsf-training.github.io/analysis-essentials/python/further_reading.html#python-and-root
Advanced Python Tutorialhttps://hsf-training.github.io/analysis-essentials/advanced-python/README.html
1: Basicshttps://hsf-training.github.io/analysis-essentials/advanced-python/10Basics.html
Basicshttps://hsf-training.github.io/analysis-essentials/advanced-python/10Basics.html#Basics
Markdownhttps://hsf-training.github.io/analysis-essentials/advanced-python/10Basics.html#Markdown
Jupyterhttps://hsf-training.github.io/analysis-essentials/advanced-python/10Basics.html#Jupyter
Importing moduleshttps://hsf-training.github.io/analysis-essentials/advanced-python/10Basics.html#Importing-modules
Advanced Python Conceptshttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html
Packing and unpacking of valueshttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Packing-and-unpacking-of-values
Context managerhttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Context-manager
Using a classhttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Using-a-class
Decorators and factorieshttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Decorators-and-factories
Exceptionshttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Exceptions
Catching exceptionshttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Catching-exceptions
Exceptions as control-flowhttps://hsf-training.github.io/analysis-essentials/advanced-python/11AdvancedPython.html#Exceptions-as-control-flow
Advanced Classeshttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html
Dunderhttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html#Dunder
selfhttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html#self
Danger zonehttps://hsf-training.github.io/analysis-essentials/advanced-python/12AdvancedClasses.html#Danger-zone
2: First look at datahttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html
Two plotting libraries?https://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Two-plotting-libraries?
Recap: Importing moduleshttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Recap:-Importing-modules
Loading datahttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Loading-data
Adding variableshttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Adding-variables
Comparing distributionshttps://hsf-training.github.io/analysis-essentials/advanced-python/20DataAndPlotting.html#Comparing-distributions
3: Multivariate Analysishttps://hsf-training.github.io/analysis-essentials/advanced-python/30Classification.html
Using a classifierhttps://hsf-training.github.io/analysis-essentials/advanced-python/30Classification.html#Using-a-classifier
4: Extension on Classificationhttps://hsf-training.github.io/analysis-essentials/advanced-python/31ClassificationExtension.html
Alternative implimentationshttps://hsf-training.github.io/analysis-essentials/advanced-python/31ClassificationExtension.html#Alternative-implimentations
Feature engineeringhttps://hsf-training.github.io/analysis-essentials/advanced-python/31ClassificationExtension.html#Feature-engineering
\(k\)-foldinghttps://hsf-training.github.io/analysis-essentials/advanced-python/31ClassificationExtension.html#k-folding
Turn this into a scipt using argparsehttps://hsf-training.github.io/analysis-essentials/advanced-python/31ClassificationExtension.html#Turn-this-into-a-scipt-using-argparse
5: Boosting to Uniformityhttps://hsf-training.github.io/analysis-essentials/advanced-python/32BoostingToUniformity.html
Loading datahttps://hsf-training.github.io/analysis-essentials/advanced-python/32BoostingToUniformity.html#Loading-data
6: Histogramshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html
Axeshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Axes
Axis Namehttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Axis-Name
Multiple dimensionshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Multiple-dimensions
Access Binshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Access-Bins
Getting Densityhttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Getting-Density
Projecting axeshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Projecting-axes
Accessing everything relevanthttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Accessing-everything-relevant
Arithmeticshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Arithmetics
Weightshttps://hsf-training.github.io/analysis-essentials/advanced-python/40Histograms.html#Weights
7: Demonstration of distribution reweightinghttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html
Downloading datahttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Downloading-data
prepare train and test sampleshttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#prepare-train-and-test-samples
train part of original distributionhttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#train-part-of-original-distribution
test part for target distributionhttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#test-part-for-target-distribution
Bins-based reweighting in n dimensionshttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Bins-based-reweighting-in-n-dimensions
Gradient Boosted Reweighterhttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Gradient-Boosted-Reweighter
GB-discriminationhttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#GB-discrimination
How to tunehttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#How-to-tune
Folding reweighterhttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#Folding-reweighter
GB discrimination for reweighting rulehttps://hsf-training.github.io/analysis-essentials/advanced-python/45DemoReweighting.html#GB-discrimination-for-reweighting-rule
8: Likelihood inferencehttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html
Scope of this tutorialhttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Scope-of-this-tutorial
Getting startedhttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Getting-started
Creating the modelhttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Creating-the-model
Plottinghttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Plotting
Losshttps://hsf-training.github.io/analysis-essentials/advanced-python/50LikelihoodInference.html#Loss
9: sPlothttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html
Simple sPlot examplehttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Simple-sPlot-example
Observed distributionshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Observed-distributions
Applying sWeightshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Applying-sWeights
More complex casehttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#More-complex-case
Splothttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Splot
Alternative: Known probabilitieshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Alternative:-Known-probabilities
Fitting doesn’t give us information about real labelshttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Fitting-doesn't-give-us-information-about-real-labels
Appying sPlothttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Appying-sPlot
Using sWeights to reconstruct initial distributionhttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Using-sWeights-to-reconstruct-initial-distribution
An important requirement of sPlothttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#An-important-requirement-of-sPlot
Derivation of sWeights (optional)https://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Derivation-of-sWeights-(optional)
Conclusionhttps://hsf-training.github.io/analysis-essentials/advanced-python/60sPlot.html#Conclusion
10: Scikit-HEPhttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html
formulate - converting expressionshttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html#formulate---converting-expressions
Particlehttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html#Particle
hepunitshttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html#hepunits
Vectorhttps://hsf-training.github.io/analysis-essentials/advanced-python/70ScikitHEPUniverse.html#Vector
Introducing the Shellhttps://hsf-training.github.io/analysis-essentials/shell/README.html
Backgroundhttps://hsf-training.github.io/analysis-essentials/shell/README.html#background
The Command-Line Interfacehttps://hsf-training.github.io/analysis-essentials/shell/README.html#the-command-line-interface
The Shellhttps://hsf-training.github.io/analysis-essentials/shell/README.html#the-shell
Why bother?https://hsf-training.github.io/analysis-essentials/shell/README.html#why-bother
Nelle’s Pipeline: Starting Pointhttps://hsf-training.github.io/analysis-essentials/shell/README.html#nelle-s-pipeline-starting-point
Navigating Files and Directorieshttps://hsf-training.github.io/analysis-essentials/shell/02-filedir.html
Working With Files and Directorieshttps://hsf-training.github.io/analysis-essentials/shell/03-create.html
Pipes and Filtershttps://hsf-training.github.io/analysis-essentials/shell/04-pipefilter.html
Loopshttps://hsf-training.github.io/analysis-essentials/shell/05-loop.html
Shell Scriptshttps://hsf-training.github.io/analysis-essentials/shell/06-script.html
Finding Thingshttps://hsf-training.github.io/analysis-essentials/shell/07-find.html
UNIX shellhttps://hsf-training.github.io/analysis-essentials/shell-extras/README.html
Using screen to keep things runninghttps://hsf-training.github.io/analysis-essentials/shell-extras/screen.html
Advanced screen topicshttps://hsf-training.github.io/analysis-essentials/shell-extras/screen2.html
Finding lost screenshttps://hsf-training.github.io/analysis-essentials/shell-extras/screen2.html#finding-lost-screens
Using tabs in screenhttps://hsf-training.github.io/analysis-essentials/shell-extras/screen2.html#using-tabs-in-screen
Persistent screen or tmux session on lxplushttps://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html
lxplus7https://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html#lxplus7
lxplus8https://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html#lxplus8
lxplus9https://hsf-training.github.io/analysis-essentials/shell-extras/persistent-screen.html#lxplus9
More about the UNIX shellhttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html
Types of shellhttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#types-of-shell
Manual pageshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#manual-pages
Environment variableshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#environment-variables
Variableshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#variables
Differences among fileshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#differences-among-files
Looping over fileshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#looping-over-files
Conditionalshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#conditionals
Linking commandshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#linking-commands
Pipes and redirectionhttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#pipes-and-redirection
Bash securityhttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#bash-security
Complexityhttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#complexity
Text viewershttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#text-viewers
Text editorshttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#text-editors
Disk spacehttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#disk-space
Over the Wire and Bandit wargamehttps://hsf-training.github.io/analysis-essentials/shell-extras/shell2.html#over-the-wire-and-bandit-wargame
Analysis automation with Snakemakehttps://hsf-training.github.io/analysis-essentials/snakemake/README.html
Documentation and environmentshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#documentation-and-environments
Workflow preservationhttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#workflow-preservation
Basic Tutorialhttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#basic-tutorial
What is a workflow?https://hsf-training.github.io/analysis-essentials/snakemake/README.html#what-is-a-workflow
Why use a workflow management system?https://hsf-training.github.io/analysis-essentials/snakemake/README.html#why-use-a-workflow-management-system
Introducing Snakemakehttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#introducing-snakemake
Re-running ruleshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#re-running-rules
Chaining ruleshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#chaining-rules
The limits of wildcardshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#the-limits-of-wildcards
Advanced Tutorialhttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#advanced-tutorial
Running scriptshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#running-scripts
Log fileshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#log-files
Config fileshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#config-files
Includeshttps://hsf-training.github.io/analysis-essentials/snakemake/README.html#includes
Githttps://hsf-training.github.io/analysis-essentials/git/README.html
Automated Version Controlhttps://hsf-training.github.io/analysis-essentials/git/01-basics.html
Setting Up Githttps://hsf-training.github.io/analysis-essentials/git/02-setup.html
Creating a Repositoryhttps://hsf-training.github.io/analysis-essentials/git/03-create.html
Tracking Changeshttps://hsf-training.github.io/analysis-essentials/git/04-changes.html
Exploring Historyhttps://hsf-training.github.io/analysis-essentials/git/05-history.html
Ignoring Thingshttps://hsf-training.github.io/analysis-essentials/git/06-ignore.html
Remotes in CERN GitLabhttps://hsf-training.github.io/analysis-essentials/git/07-gitlab.html
Sharing a repository with othershttps://hsf-training.github.io/analysis-essentials/git/08-share.html
Collaborating with Pull Requestshttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html
What is a Pull (or Merge) Requesthttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#what-is-a-pull-or-merge-request
Fork the original project repositoryhttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#fork-the-original-project-repository
Clone a remote project and its forkhttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#clone-a-remote-project-and-its-fork
Sync your local repository with remote changeshttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#sync-your-local-repository-with-remote-changes
Implement your new featurehttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#implement-your-new-feature
Push changeshttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#push-changes
Create a Pull (or Merge) Requesthttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#create-a-pull-or-merge-request
Discussing, amending, retiring a Merge Requesthttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#discussing-amending-retiring-a-merge-request
Accepting a Pull Requesthttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#accepting-a-pull-request
The social side of codinghttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#the-social-side-of-coding
Automatic testinghttps://hsf-training.github.io/analysis-essentials/git/09-pullrequests.html#automatic-testing
Conflictshttps://hsf-training.github.io/analysis-essentials/git/10-conflict.html
GitLab CIhttps://hsf-training.github.io/analysis-essentials/git/11-ci.html
Open Sciencehttps://hsf-training.github.io/analysis-essentials/git/12-open.html
Licensinghttps://hsf-training.github.io/analysis-essentials/git/13-licensing.html
Citationhttps://hsf-training.github.io/analysis-essentials/git/14-citation.html
Contributinghttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html
Contributor Agreementhttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html#contributor-agreement
How to Contributehttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html#how-to-contribute
What to Contributehttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html#what-to-contribute
Using GitHubhttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html#using-github
Other Resourceshttps://hsf-training.github.io/analysis-essentials/CONTRIBUTING.html#other-resources
Contributor Code of Conducthttps://hsf-training.github.io/analysis-essentials/CONDUCT.html
Instructional Materialhttps://hsf-training.github.io/analysis-essentials/LICENSE.html
Softwarehttps://hsf-training.github.io/analysis-essentials/LICENSE.html#software
Next https://hsf-training.github.io/analysis-essentials/python/README.html
Sphinxhttps://www.sphinx-doc.org/
themehttps://github.com/readthedocs/sphinx_rtd_theme
Read the Docshttps://readthedocs.org

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