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bam2ssj

This utility is deprecated. SJCOUNT package shall be used instead.

bamflag

This utility marks the uniquely mapped reads in a bam file by updating the FLAG field (bit 0x800) or by updating the NH tag

hm-splice-pipe

human-mouse comparative splicing pipeline

ipsa

This is IPSA package light version

ipsa-full

Integrative Pipeline for Splicing Analyses (IPSA)

irbis

A package for ultrafast detection of conserved complementary n-mers in a set of orthologous sequences

maptools

This package contains lift-over and other alignment tools

nmd

This is a repository of scripts for "Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay"

nmdnar

This is a repository of scripts for "Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay"

nmdnew

nmd paper redone for site-centric metrics

npidr

Non-parametric IDR estimation

preph.paper

Supplementary Data Files for PrePh paper

ric-contacts

This package contains a pipeline for prediction of RNA-RNA contacts from RIC-seq data.

sjcount

sjcount light version

sjcount-full

Annotation-agnostic SJ counting pipeline

stranno

trackhubs

Track hubs for the Genome Browser