epic2 out in bioinformatics

crazyhottommy / ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

MIT License

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epic2 out in bioinformatics #9

Closed endrebak closed 5 years ago

endrebak commented 5 years ago

https://github.com/biocore-ntnu/epic2

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz232/5421513

AFAIK it is by far the fastest ChIP-Seq caller :) It also fixes a bug in SICER.

Btw, you might be interested in this: https://github.com/biocore-ntnu/pyranges

Since you are using Python sometimes with Snakemake it might be more convenient than R GenomicRanges (which also is very nice :) )

crazyhottommy commented 5 years ago

congrats for the paper and thank you for sharing! I will try epic2 for some of my broad histone data. added to the list. I will take a look at pyranges as well.

endrebak commented 5 years ago

Thanks. Love this resource :)