An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data

Provides a local database of in-house and published genomes for Bacteria and Archaea from NCBI

nimfa - A Python Library for Nonnegative Matrix Factorization Techniques

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

Vector Space Modelling for Humans

A toy example for teaching Bein

Topic modeling with first-order logic (FOL) domain knowledge

Collection of stand-alone tools

some general useful python tools for genomics

RNA-seq Graph Builder is a method to reconstruct the Isoform Graph of a gene from RNA-seq data, without the genome information, where such a graph is a representation of the variants of alternative…

A novel pipeline for gene-structure prediction based on spliced alignment of transcript sequences (ESTs and mRNAs) against a genomic sequence

python package for working with immune receptor sequence data

MISO

A tool to create wiggle plots from RNA-Seq in R.

Useful functions to use with edgeR

For running and controlling miso

A program to efficiently append sequences to bed files

An R package to correct for sequence bias in RNA-Seq experiments.

A Simplistic RNA-Seq Simulator

MIA is an reference guided assembler for DNA reads as generated by recent sequencing technologies. It is designed to support unusual short reads like they come from ancient, fragmented DNA.

A efficient peak finder for high coverage ChIP-seq experiments, written in python.

A 3'-end adapter contaminant trimmer

Count number of mapped reads per reference in SAM files (often for RNA-Seq experiments)

computational biology grab-bag: messy one-off scripts for a variety of tasks

Small utilities for working with fastq sequence files.

PySeq is a python module that finds groups of items that follow a naming convention containing a numerical sequence index (e.g. fileA.001.png, fileA.002.png, fileA.003.png...) and serializes them i…

Generate simulated RNA-SEQ reads

CaPSID: Computational Pathogen Sequence IDentification