Fly Ortholog Set Matcher - Using OrthoDB v9

Provides 1:1 Ortholog Sets of chosen groups using the 2017 flybase annotations and OrthoDB v9

https://chrisstillman.github.io/OrthologSearchApp/

OrthoDB Citation:

​https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210582/

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I have accumulated a list of various piRNA/small RNA analysis tools that are available from multiple groups. These are often collaborative efforts, so please be sure to cite the appropriate papers if you use these tools. Please let me know if you want me to add anything to this list or make a correction.

Small RNA tools from the small RNA group of Johannes Gutenberg U, Mainz, Germany
Unitas, proTRAC, PPmeter, Phaser

http://www.smallrnagroup.uni-mainz.de/

TEsmall (generic small RNA analysis with piRNA and siRNA TE methods)

https://github.com/mhammell-laboratory/tesmall


piPipes

https://github.com/bowhan/piPipes
Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325541/

TEtools

https://github.com/l-modolo/TEtools
Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389681/

sRNAPipe

https://github.com/brassetjensen/sRNAPipe
Galaxy Toolshed:  https://toolshed.g2.bx.psu.edu/repository?repository_id=13a327665795142c
Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069783/

Computing siRNA and piRNA overlap signatures

Paper: ​https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12

Samuel H Lewis GitHub

https://github.com/SamuelHLewis/sRNAplot
Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5732027/

Blaise Li piRNA pipeline:

https://bitbucket.org/blaiseli/pirna-pipeline
Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182186/

PILFER

https://github.com/rishavray/PILFER
Paper: https://www.ncbi.nlm.nih.gov/pubmed/29268962

PingPongPro

https://github.com/suhrig/pingpongpro
Paper: https://www.ncbi.nlm.nih.gov/pubmed/29985981