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bamtools

C++ API & command-line toolkit for working with BAM data

bicg_2017

bicg_scwgs

biclustering

biobambam2

Tools for early stage alignment file processing

bioconda-recipes

Conda recipes for the bioconda channel.

blossomv

Blossom V python wrapper

cancersimulator

cbw_can_scdna_2021

cgpbattenberg

Battenberg algorithm and associated implementation script

citup

Clonality inference in multiple tumor samples using phylogeny

defuse

An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

destruct

Accurate Rearrangement Detection using Breakpoint Specific Realignment

dwgsim

Whole Genome Simulator for Next-Generation Sequencing

genevector

Vector representations of gene co-expression in single cell RNAseq.

genotype_and_phase_snps

Genotype and phase snps workflow

ggnome

R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework

notedown

Markdown <=> IPython Notebook

oncokb-annotator

Annotates variants in MAF with OncoKB annotation.

openondemandapps

Open OnDemand Apps

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.

pybam

python bam reader

pypeliner

pyro_tutorial

A tutorial on the basics of the pyro probabilistic programming language

remixt

Clone-specific genomic structure estimation in cancer

scicone

Single-cell copy number calling and event history reconstruction.

sciphi