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Title: History for scripts - GreenleafLab/array_analysis · GitHub

Open Graph Title: History for scripts - GreenleafLab/array_analysis

X Title: History for scripts - GreenleafLab/array_analysis

Description: Snakemake pipeline for Greenleaf lab array preprocessing. - History for scripts - GreenleafLab/array_analysis

Open Graph Description: Snakemake pipeline for Greenleaf lab array preprocessing. - History for scripts - GreenleafLab/array_analysis

X Description: Snakemake pipeline for Greenleaf lab array preprocessing. - History for scripts - GreenleafLab/array_analysis

Opengraph URL: https://github.com/GreenleafLab/array_analysis

X: @github

direct link

Domain: github.com

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Links:

Skip to content	https://github.com/GreenleafLab/array_analysis/commits/main/scripts#start-of-content
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array_analysis	https://github.com/GreenleafLab/array_analysis/commits
scripts	https://github.com/GreenleafLab/array_analysis/commits/main/scripts
main	https://github.com/GreenleafLab/array_analysis/tree/main
add singularity container	https://github.com/GreenleafLab/array_analysis/commit/3b2108b42d504fe524f77b12577b2e510363bc83
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
3b2108b	https://github.com/GreenleafLab/array_analysis/commit/3b2108b42d504fe524f77b12577b2e510363bc83
	https://github.com/GreenleafLab/array_analysis/blob/3b2108b42d504fe524f77b12577b2e510363bc83/scripts
	https://github.com/GreenleafLab/array_analysis/tree/3b2108b42d504fe524f77b12577b2e510363bc83
Edited files to analyze 20220314 data	https://github.com/GreenleafLab/array_analysis/commit/19af34fccb3ca953d0013b440c9910b83846d091
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
19af34f	https://github.com/GreenleafLab/array_analysis/commit/19af34fccb3ca953d0013b440c9910b83846d091
	https://github.com/GreenleafLab/array_analysis/blob/19af34fccb3ca953d0013b440c9910b83846d091/scripts
	https://github.com/GreenleafLab/array_analysis/tree/19af34fccb3ca953d0013b440c9910b83846d091
fairly stable version for fitting	https://github.com/GreenleafLab/array_analysis/commit/d49d1b3a34c02187e6ef4bc438832006eb2f6fe6
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
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	https://github.com/GreenleafLab/array_analysis/blob/d49d1b3a34c02187e6ef4bc438832006eb2f6fe6/scripts
	https://github.com/GreenleafLab/array_analysis/tree/d49d1b3a34c02187e6ef4bc438832006eb2f6fe6
iron out the whole fitting process	https://github.com/GreenleafLab/array_analysis/commit/34745912afcbc7e7c8ecfcf4650a914d83bd3a9b
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
3474591	https://github.com/GreenleafLab/array_analysis/commit/34745912afcbc7e7c8ecfcf4650a914d83bd3a9b
	https://github.com/GreenleafLab/array_analysis/blob/34745912afcbc7e7c8ecfcf4650a914d83bd3a9b/scripts
	https://github.com/GreenleafLab/array_analysis/tree/34745912afcbc7e7c8ecfcf4650a914d83bd3a9b
first version of refine fitting plus making a smaller cluster annotation file from CPseq	https://github.com/GreenleafLab/array_analysis/commit/8a2b9c815112ecb8dcfebe886dd7fc73bcf1dc64
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
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	https://github.com/GreenleafLab/array_analysis/blob/8a2b9c815112ecb8dcfebe886dd7fc73bcf1dc64/scripts
	https://github.com/GreenleafLab/array_analysis/tree/8a2b9c815112ecb8dcfebe886dd7fc73bcf1dc64
implement fit fmax fmin distribution	https://github.com/GreenleafLab/array_analysis/commit/88a7a4052a32632f8108d87e25ddcfefa128daf6
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
88a7a40	https://github.com/GreenleafLab/array_analysis/commit/88a7a4052a32632f8108d87e25ddcfefa128daf6
	https://github.com/GreenleafLab/array_analysis/blob/88a7a4052a32632f8108d87e25ddcfefa128daf6/scripts
	https://github.com/GreenleafLab/array_analysis/tree/88a7a4052a32632f8108d87e25ddcfefa128daf6
Updated bootstrapfit file and started to work on findfmaxfmin	https://github.com/GreenleafLab/array_analysis/commit/dbaca18da89c7900ee3cc727e172ea5617a6d80e
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
dbaca18	https://github.com/GreenleafLab/array_analysis/commit/dbaca18da89c7900ee3cc727e172ea5617a6d80e
	https://github.com/GreenleafLab/array_analysis/blob/dbaca18da89c7900ee3cc727e172ea5617a6d80e/scripts
	https://github.com/GreenleafLab/array_analysis/tree/dbaca18da89c7900ee3cc727e172ea5617a6d80e
Fix sequencingResult bug in Snakefile and rerun Oct6 alignment with the correct nupack annotation file	https://github.com/GreenleafLab/array_analysis/commit/5b59e8bcf9cacb8100cc50cf0b3b13647588d310
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
5b59e8b	https://github.com/GreenleafLab/array_analysis/commit/5b59e8bcf9cacb8100cc50cf0b3b13647588d310
	https://github.com/GreenleafLab/array_analysis/blob/5b59e8bcf9cacb8100cc50cf0b3b13647588d310/scripts
	https://github.com/GreenleafLab/array_analysis/tree/5b59e8bcf9cacb8100cc50cf0b3b13647588d310
first run of bootstrapFitFile	https://github.com/GreenleafLab/array_analysis/commit/b4e9b1c240647ac8ab3686a6ffce17a3424756fd
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
b4e9b1c	https://github.com/GreenleafLab/array_analysis/commit/b4e9b1c240647ac8ab3686a6ffce17a3424756fd
	https://github.com/GreenleafLab/array_analysis/blob/b4e9b1c240647ac8ab3686a6ffce17a3424756fd/scripts
	https://github.com/GreenleafLab/array_analysis/tree/b4e9b1c240647ac8ab3686a6ffce17a3424756fd
post array analysis for Nov11 chip	https://github.com/GreenleafLab/array_analysis/commit/2bc64b7ba537e0d9012bc7ccf344014d4ff61415
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
2bc64b7	https://github.com/GreenleafLab/array_analysis/commit/2bc64b7ba537e0d9012bc7ccf344014d4ff61415
	https://github.com/GreenleafLab/array_analysis/blob/2bc64b7ba537e0d9012bc7ccf344014d4ff61415/scripts
	https://github.com/GreenleafLab/array_analysis/tree/2bc64b7ba537e0d9012bc7ccf344014d4ff61415
single clulster fitting on sherlock	https://github.com/GreenleafLab/array_analysis/commit/cfb5a9a8959c0b042fb6fded11603af3433ae14c
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
cfb5a9a	https://github.com/GreenleafLab/array_analysis/commit/cfb5a9a8959c0b042fb6fded11603af3433ae14c
	https://github.com/GreenleafLab/array_analysis/blob/cfb5a9a8959c0b042fb6fded11603af3433ae14c/scripts
	https://github.com/GreenleafLab/array_analysis/tree/cfb5a9a8959c0b042fb6fded11603af3433ae14c
Implement single cluster fit with new version of lmfit	https://github.com/GreenleafLab/array_analysis/commit/4403bf18145727b078f4446921002d821a175f29
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
4403bf1	https://github.com/GreenleafLab/array_analysis/commit/4403bf18145727b078f4446921002d821a175f29
	https://github.com/GreenleafLab/array_analysis/blob/4403bf18145727b078f4446921002d821a175f29/scripts
	https://github.com/GreenleafLab/array_analysis/tree/4403bf18145727b078f4446921002d821a175f29
version before I gave up simply modifying Sarah's codebase	https://github.com/GreenleafLab/array_analysis/commit/231d1fa3d6adf7502f8ec68e8581de47e6943003
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
231d1fa	https://github.com/GreenleafLab/array_analysis/commit/231d1fa3d6adf7502f8ec68e8581de47e6943003
	https://github.com/GreenleafLab/array_analysis/blob/231d1fa3d6adf7502f8ec68e8581de47e6943003/scripts
	https://github.com/GreenleafLab/array_analysis/tree/231d1fa3d6adf7502f8ec68e8581de47e6943003
merge fitting scripts on main to nnn	https://github.com/GreenleafLab/array_analysis/commit/8a0e15755960b1df610191421577cd6d1a03dc47
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
8a0e157	https://github.com/GreenleafLab/array_analysis/commit/8a0e15755960b1df610191421577cd6d1a03dc47
	https://github.com/GreenleafLab/array_analysis/blob/8a0e15755960b1df610191421577cd6d1a03dc47/scripts
	https://github.com/GreenleafLab/array_analysis/tree/8a0e15755960b1df610191421577cd6d1a03dc47
Implemented single cluster melt curve fit	https://github.com/GreenleafLab/array_analysis/commit/ddf3a277da976366e1471567f365a75145c06ccb
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
ddf3a27	https://github.com/GreenleafLab/array_analysis/commit/ddf3a277da976366e1471567f365a75145c06ccb
	https://github.com/GreenleafLab/array_analysis/blob/ddf3a277da976366e1471567f365a75145c06ccb/scripts
	https://github.com/GreenleafLab/array_analysis/tree/ddf3a277da976366e1471567f365a75145c06ccb
Converted fitting scripts to py3 and modified single cluster fit	https://github.com/GreenleafLab/array_analysis/commit/97d7b6bdad43b6cb9cca0ad28eaebc4964d48410
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
97d7b6b	https://github.com/GreenleafLab/array_analysis/commit/97d7b6bdad43b6cb9cca0ad28eaebc4964d48410
	https://github.com/GreenleafLab/array_analysis/blob/97d7b6bdad43b6cb9cca0ad28eaebc4964d48410/scripts
	https://github.com/GreenleafLab/array_analysis/tree/97d7b6bdad43b6cb9cca0ad28eaebc4964d48410
Merge branch 'nnn' of https://github.com/keyuxi/array_analysis into nnn	https://github.com/GreenleafLab/array_analysis/commit/7c714bef8a39aa880f0cde091fb78938bfa1c14a
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
7c714be	https://github.com/GreenleafLab/array_analysis/commit/7c714bef8a39aa880f0cde091fb78938bfa1c14a
	https://github.com/GreenleafLab/array_analysis/blob/7c714bef8a39aa880f0cde091fb78938bfa1c14a/scripts
	https://github.com/GreenleafLab/array_analysis/tree/7c714bef8a39aa880f0cde091fb78938bfa1c14a
Add normalize signal script	https://github.com/GreenleafLab/array_analysis/commit/f5fe46dd4993314c315692f068606fbeb0c92e87
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
f5fe46d	https://github.com/GreenleafLab/array_analysis/commit/f5fe46dd4993314c315692f068606fbeb0c92e87
	https://github.com/GreenleafLab/array_analysis/blob/f5fe46dd4993314c315692f068606fbeb0c92e87/scripts
	https://github.com/GreenleafLab/array_analysis/tree/f5fe46dd4993314c315692f068606fbeb0c92e87
made script copies for nnn fitting	https://github.com/GreenleafLab/array_analysis/commit/0db1403180f2ed91430448d6320fd003b2d70f57
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
0db1403	https://github.com/GreenleafLab/array_analysis/commit/0db1403180f2ed91430448d6320fd003b2d70f57
	https://github.com/GreenleafLab/array_analysis/blob/0db1403180f2ed91430448d6320fd003b2d70f57/scripts
	https://github.com/GreenleafLab/array_analysis/tree/0db1403180f2ed91430448d6320fd003b2d70f57
add normalization script	https://github.com/GreenleafLab/array_analysis/commit/27b922c1a5b589ec96f2f2b8d3e7414bd670ea0f
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
27b922c	https://github.com/GreenleafLab/array_analysis/commit/27b922c1a5b589ec96f2f2b8d3e7414bd670ea0f
	https://github.com/GreenleafLab/array_analysis/blob/27b922c1a5b589ec96f2f2b8d3e7414bd670ea0f/scripts
	https://github.com/GreenleafLab/array_analysis/tree/27b922c1a5b589ec96f2f2b8d3e7414bd670ea0f
clean up scripts	https://github.com/GreenleafLab/array_analysis/commit/3c042794f1c5851849c5d132df6937924a2ca689
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
3c04279	https://github.com/GreenleafLab/array_analysis/commit/3c042794f1c5851849c5d132df6937924a2ca689
	https://github.com/GreenleafLab/array_analysis/blob/3c042794f1c5851849c5d132df6937924a2ca689/scripts
	https://github.com/GreenleafLab/array_analysis/tree/3c042794f1c5851849c5d132df6937924a2ca689
update sequence alignment	https://github.com/GreenleafLab/array_analysis/commit/8f0e08011b209fcded90c9331ddfa97c4b2d88e3
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
8f0e080	https://github.com/GreenleafLab/array_analysis/commit/8f0e08011b209fcded90c9331ddfa97c4b2d88e3
	https://github.com/GreenleafLab/array_analysis/blob/8f0e08011b209fcded90c9331ddfa97c4b2d88e3/scripts
	https://github.com/GreenleafLab/array_analysis/tree/8f0e08011b209fcded90c9331ddfa97c4b2d88e3
changed 3prime align to current version	https://github.com/GreenleafLab/array_analysis/commit/14cf1406dac10a314561bb2466b05aacd18bc618
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
14cf140	https://github.com/GreenleafLab/array_analysis/commit/14cf1406dac10a314561bb2466b05aacd18bc618
	https://github.com/GreenleafLab/array_analysis/blob/14cf1406dac10a314561bb2466b05aacd18bc618/scripts
	https://github.com/GreenleafLab/array_analysis/tree/14cf1406dac10a314561bb2466b05aacd18bc618
add pre-array or post-array option	https://github.com/GreenleafLab/array_analysis/commit/33e97f929a9a42d859de03741d5fd6adb1f51be4
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
33e97f9	https://github.com/GreenleafLab/array_analysis/commit/33e97f929a9a42d859de03741d5fd6adb1f51be4
	https://github.com/GreenleafLab/array_analysis/blob/33e97f929a9a42d859de03741d5fd6adb1f51be4/scripts
	https://github.com/GreenleafLab/array_analysis/tree/33e97f929a9a42d859de03741d5fd6adb1f51be4
fixed CPseq output file name discrepancy issue	https://github.com/GreenleafLab/array_analysis/commit/fb3786d713c848897b8ce454bc579ecd1ae67f5e
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
fb3786d	https://github.com/GreenleafLab/array_analysis/commit/fb3786d713c848897b8ce454bc579ecd1ae67f5e
	https://github.com/GreenleafLab/array_analysis/blob/fb3786d713c848897b8ce454bc579ecd1ae67f5e/scripts
	https://github.com/GreenleafLab/array_analysis/tree/fb3786d713c848897b8ce454bc579ecd1ae67f5e
working version for aligning NNNlib2b_run3 Nov11	https://github.com/GreenleafLab/array_analysis/commit/1f16a0b4db1c0b1438ae3ff190fcff1b4fc487f5
1f16a0b	https://github.com/GreenleafLab/array_analysis/commit/1f16a0b4db1c0b1438ae3ff190fcff1b4fc487f5
	https://github.com/GreenleafLab/array_analysis/blob/1f16a0b4db1c0b1438ae3ff190fcff1b4fc487f5/scripts
	https://github.com/GreenleafLab/array_analysis/tree/1f16a0b4db1c0b1438ae3ff190fcff1b4fc487f5
add NNNlib2b Nov11 stuffs	https://github.com/GreenleafLab/array_analysis/commit/8c8c099b85649722a19bb1c2202a8d3a119d3f3b
8c8c099	https://github.com/GreenleafLab/array_analysis/commit/8c8c099b85649722a19bb1c2202a8d3a119d3f3b
	https://github.com/GreenleafLab/array_analysis/blob/8c8c099b85649722a19bb1c2202a8d3a119d3f3b/scripts
	https://github.com/GreenleafLab/array_analysis/tree/8c8c099b85649722a19bb1c2202a8d3a119d3f3b
working version for merging CPfluor files to CPseries	https://github.com/GreenleafLab/array_analysis/commit/07eb36464e00f69aea4d4ec3474c92b4f6bdcc3d
07eb364	https://github.com/GreenleafLab/array_analysis/commit/07eb36464e00f69aea4d4ec3474c92b4f6bdcc3d
	https://github.com/GreenleafLab/array_analysis/blob/07eb36464e00f69aea4d4ec3474c92b4f6bdcc3d/scripts
	https://github.com/GreenleafLab/array_analysis/tree/07eb36464e00f69aea4d4ec3474c92b4f6bdcc3d
quantify images working version	https://github.com/GreenleafLab/array_analysis/commit/e367997b0d00ca72515ad620072c460dc42a9558
e367997	https://github.com/GreenleafLab/array_analysis/commit/e367997b0d00ca72515ad620072c460dc42a9558
	https://github.com/GreenleafLab/array_analysis/blob/e367997b0d00ca72515ad620072c460dc42a9558/scripts
	https://github.com/GreenleafLab/array_analysis/tree/e367997b0d00ca72515ad620072c460dc42a9558
Merge branch 'nnn' of git+ssh://github.com/keyuxi/array_analysis into nnn	https://github.com/GreenleafLab/array_analysis/commit/d15c7f1d621ff21015740a1016ad4efa95f0018c
d15c7f1	https://github.com/GreenleafLab/array_analysis/commit/d15c7f1d621ff21015740a1016ad4efa95f0018c
	https://github.com/GreenleafLab/array_analysis/blob/d15c7f1d621ff21015740a1016ad4efa95f0018c/scripts
	https://github.com/GreenleafLab/array_analysis/tree/d15c7f1d621ff21015740a1016ad4efa95f0018c
edit on sherlock	https://github.com/GreenleafLab/array_analysis/commit/0341a21a59ef3c3f0c1746a249157ac46ab7fb55
0341a21	https://github.com/GreenleafLab/array_analysis/commit/0341a21a59ef3c3f0c1746a249157ac46ab7fb55
	https://github.com/GreenleafLab/array_analysis/blob/0341a21a59ef3c3f0c1746a249157ac46ab7fb55/scripts
	https://github.com/GreenleafLab/array_analysis/tree/0341a21a59ef3c3f0c1746a249157ac46ab7fb55
sample sheet	https://github.com/GreenleafLab/array_analysis/commit/27fdb679dfa418eddea4f26dad839f3a199670e1
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
27fdb67	https://github.com/GreenleafLab/array_analysis/commit/27fdb679dfa418eddea4f26dad839f3a199670e1
	https://github.com/GreenleafLab/array_analysis/blob/27fdb679dfa418eddea4f26dad839f3a199670e1/scripts
	https://github.com/GreenleafLab/array_analysis/tree/27fdb679dfa418eddea4f26dad839f3a199670e1
quickly plotted fiducials in tiles	https://github.com/GreenleafLab/array_analysis/commit/5b0f6d67283d48e3e3c71470efc9726234b0b22b
5b0f6d6	https://github.com/GreenleafLab/array_analysis/commit/5b0f6d67283d48e3e3c71470efc9726234b0b22b
	https://github.com/GreenleafLab/array_analysis/blob/5b0f6d67283d48e3e3c71470efc9726234b0b22b/scripts
	https://github.com/GreenleafLab/array_analysis/tree/5b0f6d67283d48e3e3c71470efc9726234b0b22b
update plot function	https://github.com/GreenleafLab/array_analysis/commit/a7181d693a982ffd8ffcbc130bcea4bcbb590217
	https://github.com/keyuxi
keyuxi	https://github.com/GreenleafLab/array_analysis/commits?author=keyuxi
a7181d6	https://github.com/GreenleafLab/array_analysis/commit/a7181d693a982ffd8ffcbc130bcea4bcbb590217
	https://github.com/GreenleafLab/array_analysis/blob/a7181d693a982ffd8ffcbc130bcea4bcbb590217/scripts
	https://github.com/GreenleafLab/array_analysis/tree/a7181d693a982ffd8ffcbc130bcea4bcbb590217
add array_tools and plotting	https://github.com/GreenleafLab/array_analysis/commit/9cdbedaf6b257f1878dd9e4dfef314165ea4aaed
9cdbeda	https://github.com/GreenleafLab/array_analysis/commit/9cdbedaf6b257f1878dd9e4dfef314165ea4aaed
	https://github.com/GreenleafLab/array_analysis/blob/9cdbedaf6b257f1878dd9e4dfef314165ea4aaed/scripts
	https://github.com/GreenleafLab/array_analysis/tree/9cdbedaf6b257f1878dd9e4dfef314165ea4aaed
Next	https://github.com/GreenleafLab/array_analysis/commits/main/scripts?after=998985b552b8aa71eb0a3717ee809aab575cf3ab+34
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