René's URL Explorer Experiment

Title: GitHub - oushujun/EDTA: Extensive de-novo TE Annotator

Open Graph Title: GitHub - oushujun/EDTA: Extensive de-novo TE Annotator

X Title: GitHub - oushujun/EDTA: Extensive de-novo TE Annotator

Description: Extensive de-novo TE Annotator . Contribute to oushujun/EDTA development by creating an account on GitHub.

Open Graph Description: Extensive de-novo TE Annotator . Contribute to oushujun/EDTA development by creating an account on GitHub.

X Description: Extensive de-novo TE Annotator . Contribute to oushujun/EDTA development by creating an account on GitHub.

Opengraph URL: https://github.com/oushujun/EDTA

X: @github

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genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
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panEDTA.sh	https://patch-diff.githubusercontent.com/oushujun/EDTA/blob/master/panEDTA.sh
README	https://patch-diff.githubusercontent.com/oushujun/EDTA
GPL-3.0 license	https://patch-diff.githubusercontent.com/oushujun/EDTA
	https://anaconda.org/bioconda/edta
	https://github.com/oushujun/EDTA/blob/master/LICENSE
	https://anaconda.org/bioconda/edta
	https://anaconda.org/bioconda/edta
	https://patch-diff.githubusercontent.com/oushujun/EDTA#the-extensive-de-novo-te-annotator-edta
	https://patch-diff.githubusercontent.com/oushujun/EDTA#table-of-contents
The Extensive de novo TE Annotator (EDTA)	https://patch-diff.githubusercontent.com/oushujun/EDTA#the-extensive-de-novo-te-annotator-edta
Table of Contents	https://patch-diff.githubusercontent.com/oushujun/EDTA#table-of-contents
Introduction	https://patch-diff.githubusercontent.com/oushujun/EDTA#introduction
Installation	https://patch-diff.githubusercontent.com/oushujun/EDTA#installation
Install with conda/mamba (Linux64)	https://patch-diff.githubusercontent.com/oushujun/EDTA#install-with-condamamba-linux64
Install with Singularity (good for HPC users)	https://patch-diff.githubusercontent.com/oushujun/EDTA#install-with-singularity-good-for-hpc-users
Install with Docker (good for root/macOS/Apple M-chip users)	https://patch-diff.githubusercontent.com/oushujun/EDTA#install-with-docker-good-for-rootmacosapple-m-chip-users
Testing	https://patch-diff.githubusercontent.com/oushujun/EDTA#testing
Inputs	https://patch-diff.githubusercontent.com/oushujun/EDTA#inputs
Outputs	https://patch-diff.githubusercontent.com/oushujun/EDTA#outputs
EDTA Usage	https://patch-diff.githubusercontent.com/oushujun/EDTA#edta-usage
From head to toe	https://patch-diff.githubusercontent.com/oushujun/EDTA#from-head-to-toe
Divide and conquer	https://patch-diff.githubusercontent.com/oushujun/EDTA#divide-and-conquer
Protips and self-diagnosis	https://patch-diff.githubusercontent.com/oushujun/EDTA#protips-and-self-diagnosis
panEDTA usage	https://patch-diff.githubusercontent.com/oushujun/EDTA#panedta-usage
Benchmark	https://patch-diff.githubusercontent.com/oushujun/EDTA#benchmark
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Acknowledgements	https://patch-diff.githubusercontent.com/oushujun/EDTA#acknowledgements
	https://patch-diff.githubusercontent.com/oushujun/EDTA#introduction
example	https://github.com/HuffordLab/NAM-genomes/tree/master/te-annotation
	https://patch-diff.githubusercontent.com/oushujun/EDTA#installation
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	https://patch-diff.githubusercontent.com/oushujun/EDTA#install-with-condamamba-linux64
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	https://patch-diff.githubusercontent.com/oushujun/EDTA#install-with-singularity-good-for-hpc-users
BioContainers	https://quay.io/repository/biocontainers/edta?tab=tags
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	https://patch-diff.githubusercontent.com/oushujun/EDTA#install-with-docker-good-for-rootmacosapple-m-chip-users
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	https://patch-diff.githubusercontent.com/oushujun/EDTA#testing
collection of issues	https://github.com/oushujun/EDTA/wiki/Installations,-builds,-and-tests-Q&A
	https://patch-diff.githubusercontent.com/oushujun/EDTA#inputs
How to prepare a curated library to maximize the efficacy of EDTA	https://github.com/oushujun/EDTA/wiki/How-to-prepare-a-curated-library-to-maximize-the-efficacy-of-EDTA
	https://patch-diff.githubusercontent.com/oushujun/EDTA#outputs
rice library	https://patch-diff.githubusercontent.com/oushujun/EDTA/blob/master/database/rice7.0.0.liban
Wicker et al. (2007)	https://www.nature.com/articles/nrg2165
TE sequence ontology file	https://patch-diff.githubusercontent.com/oushujun/EDTA/blob/master/bin/TE_Sequence_Ontology.txt
	https://patch-diff.githubusercontent.com/oushujun/EDTA#edta-usage
	https://patch-diff.githubusercontent.com/oushujun/EDTA#from-head-to-toe
	https://patch-diff.githubusercontent.com/oushujun/EDTA#divide-and-conquer
	https://patch-diff.githubusercontent.com/oushujun/EDTA#protips-and-self-diagnosis
Wiki page	https://github.com/oushujun/EDTA/wiki
	https://patch-diff.githubusercontent.com/oushujun/EDTA#panedta-usage
wiki	https://github.com/oushujun/EDTA/wiki/Making-sense-of-EDTA-usage-and-outputs---Q&A
	https://patch-diff.githubusercontent.com/oushujun/EDTA#benchmark
	https://patch-diff.githubusercontent.com/oushujun/EDTA#citations
Genome Biol. 20(1): 275.	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
Genome Research	https://doi.org/10.1101/gr.278131.123
	https://patch-diff.githubusercontent.com/oushujun/EDTA#other-resources
rice genome here	http://rice.uga.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/
	https://patch-diff.githubusercontent.com/oushujun/EDTA#questions-and-issues
Q&A page	https://github.com/oushujun/EDTA/wiki
Issues	https://github.com/oushujun/EDTA/issues
here	https://github.com/oushujun/EDTA/issues/15
	https://patch-diff.githubusercontent.com/oushujun/EDTA#acknowledgements
Jacques Dainat	https://github.com/Juke34
Qiushi Li	https://github.com/QiushiLi
Zhigui Bao	https://github.com/baozg
Philipp Bayer	https://github.com/philippbayer
Nick Carleson	https://github.com/Neato-Nick
@aderzelle	https://github.com/aderzelle
Sanzhen Liu	https://github.com/liu3zhenlab
Zhougeng Xu	https://github.com/xuzhougeng
Shun Wang	https://github.com/wangshun1121
Nancy Manchanda	https://github.com/nm100
Eric Burgueño	https://github.com/eburgueno
Sergei Ryazansky	https://github.com/DrHogart
genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
benchmarking	https://patch-diff.githubusercontent.com/topics/benchmarking
pipeline	https://patch-diff.githubusercontent.com/topics/pipeline
genome-annotation	https://patch-diff.githubusercontent.com/topics/genome-annotation
transposable-elements	https://patch-diff.githubusercontent.com/topics/transposable-elements
Readme	https://patch-diff.githubusercontent.com/oushujun/EDTA#readme-ov-file
GPL-3.0 license	https://patch-diff.githubusercontent.com/oushujun/EDTA#GPL-3.0-1-ov-file
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Releases 17	https://patch-diff.githubusercontent.com/oushujun/EDTA/releases
v2.2.2 Remembering Faye Latest Nov 25, 2024	https://patch-diff.githubusercontent.com/oushujun/EDTA/releases/tag/v2.2.2
+ 16 releases	https://patch-diff.githubusercontent.com/oushujun/EDTA/releases
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Docs	https://docs.github.com/
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