noahpieta

bioawk

BWK awk modified for biological data

Biopython-cn

Biopython Tutorial Chinese Translation

CIRCexplorer

A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147)

CIRCexplorer2

circular RNA analysis toolset

CIRCfinder

A pipeline to map junction reads for circular intronic RNAs (ciRNAs)

CIRCpseudo

Pipeline for circRNA-derived pseudogenes

CircTest

CircRNA testing and ploting R package

clipper

A tool to identify CLIP-seq peaks

conda

OS-agnostic, system-level binary package manager and ecosystem

genome_coverage_plotter

Simple script to generate whole-genome coverage plots

gtfparse

Parsing tools for GTF (gene transfer format) files

icSHAPE

icSHAPE pipeline

JunctionSeq

The JunctionSeq R package is a powerful tool for testing and visualizing differential usage of exons and splice junctions in next-generation, high-throughput RNA-Seq experiments.

majiq-voila-elife

Repository to support the reproducibility of the results contained in Vaquero et al. manuscript published in eLife

MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation

psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

python-boilerplate-template

PasteScript template for initializing a new buildout/pytest/travis/setuptools-enabled Python project

Python-mode-klen

python mode

RiA2

Source code for R in Action, Second Edition

rnaseqlib

RNA-Seq pipeline

sailfish

Rapid Mapping-based Isoform Quantification from RNA-Seq Reads

scilife-python-course

tophat

Spliced read mapper for RNA-Seq

weblogo

WebLogo 3: Sequence Logos redrawn