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/
*********
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
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/
*********
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