dawe

pymc

Bayesian Modeling and Probabilistic Programming in Python

thrust

[ARCHIVED] The C++ parallel algorithms library. See https://github.com/NVIDIA/cccl

seurat

R toolkit for single cell genomics

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

MACS

MACS -- Model-based Analysis of ChIP-Seq

kallisto

Near-optimal RNA-Seq quantification

powerlaw

bamtools

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

PyVCF

A Variant Call Format reader for Python.

MOFA2

Multi-Omics Factor Analysis

epiScanpy

Episcanpy: Epigenomics Single Cell Analysis in Python

bedtools

A powerful toolset for genome arithmetic.

bustools

Tools for working with BUS files

metaseq

Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data

scanpy_usage

Scanpy use cases.

UMICollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.

biobambam

Tools for bam file processing

filo

Useful FILe and stream Operations

isaac_variant_caller

This project is deprecated, please see strelka2 at https://github.com/Illumina/strelka

isaac_aligner

Isaac Genome Alignment Software

SnapTools

A module for working with snap files in Python

Holes

A Python module for detecting, analysing and visualising persistent homological features of complex networks

stitch

Overlap assembler of paired-end DNA sequences generated by Illumina

python-caterva

Python wrapper for Caterva. Still preliminary.

gee_fu

An extensible Ruby on Rails web-service application and database for visualising HTGS data

Spectacle

Spectral learning for Annotating Chromatin Labels and Epigenomes

MIIC

HiGraph.js

retreat-matcher

CDPC