etal

cnvkit

Copy number variant detection from targeted DNA sequencing

cnvkit-examples

Example datasets for CNVkit (http://github.com/etal/cnvkit)

biopython

Eric's personal Biopython branch

biofrills

Biomolecular sequence analysis modules -- a supplement to Biopython

bodymap

Draw anatomical maps.

fammer

For protein superfamily sequence profile alignment and curation.

bioseq.js

Simple biomolecular sequence processing for Javascript

cnvkit-dnanexus

DNAnexus app for CNVkit

biocma

Consensus Multiple Alignment format, using Biopython classes.

cladecompare

IGV

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

seaborn

Statistical data visualization using matplotlib

THetA

Tumor Heterogeneity Analysis (THetA) is an algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data.

lofsigrank

Identify potential tumor suppressors from the relative burden of loss-of-function mutations.

AAV

Scripts for analyzing PacBio AAV sequences

bcbio-nextgen

Validated, scalable, community developed variant calling and RNA-seq analysis

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics

Tools for bioinformatics

biopython.github.io

Source of biopython.org website, migrated from MediaWiki

doc2wdl

Create WDL tasks from CLI help text

dx-toolkit

DNAnexus platform client libraries

etal.github.io

genomelake

Simple and efficient access to genomic data for deep learning models.

pytest-wdl

WDL plugin for pytest

talks

vcf-scripts