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pbdagcon

A sequence consensus algorithm implementation based on using directed acyclic graphs to encode multiple sequence alignment

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

pipeline_analysis_chipseq

A pipeline to analyse chipseq data.

psichomics

Interactive R package to quantify, analyse and visualise alternative splicing data

pydata-book

Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media

pyleaf

A Python pipeline management system

r-pkgs

Building R packages

r4ds

R for data science

reactionminer

Tool to predict (bio)chemical reactions using graph mining.

repenrich

RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.

reshape

An R package to flexible rearrange, reshape and aggregate data

rhipe

R and Hadoop Integrated Programming Environment

rmats-turbo

rnacocktail

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rsem

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

rstudio

RStudio is an integrated development environment (IDE) for R

rtcga

Package offers download and integration of the variety & volume of TCGA data.

rtsne

R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding

safe-java

Spatial Analysis of Functional Enrichment (SAFE)

scikit-learn

scikit-learn: machine learning in Python

scrna-tools

Table of software for the analysis of single-cell RNA-seq data.

seqware

This is the SeqWare Project's main repo.

shiny

Easy interactive web applications with R

shiny-examples

shiny-server

Host Shiny applications over the web.

sickle

Windowed Adaptive Trimming for fastq files using quality

smite

This repo contains the R package SMITE.

smrt-analysis

SMRT® Analysis is PacBio's bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data

splicetools