wgsim

igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer

GSEApy

Gene Set Enrichment Analysis in Python

prescient

Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.

one-key-hidpi

Enable macOS HiDPI and have a native setting.

BetterDisplay

Unlock your displays on your Mac! Flexible HiDPI scaling, XDR/HDR extra brightness, virtual screens, DDC control, extra dimming, PIP/streaming, EDID override and lots more!

python-louvain

Louvain Community Detection

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

msisensor-rna

MSIsensor-RNA: Microsatellite instability detection using RNA sequencing data

pairtree

Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples and cancer cell subpopulations than other algorithms, and on producing concise and informative interactive characterizations of posterior uncertainty.

phylowgs

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

CloneFinder

CloneFinderAPI

API for the Clone Finder application

rgsam

Infer read-group information from read names in SAM or FASTQ file.

AUCell

AUCell: score single cells with gene regulatory networks

gficf

An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization

Interactive-Enrichment-Analysis

A set of Shiny apps to provide interactive enrichment analysis and exploration of results.

toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

flammkuchen

Flexible HDF5 saving/loading library forked from deepdish (University of Chicago) and maintained by the Portugues lab

subset-bam

bwa-mem2

The next version of bwa-mem

Monopogen

SNV calling from single cell sequencing

SCmut

msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

msisensor2

Microsatellite instability (MSI) detection for tumor only data.

msisensor

microsatellite instability detection using tumor only or paired tumor-normal data

NGS

Next-Gen Sequencing tools from the Horvath Lab

scAllele

datahub-study-curation-tools

Contains tools used by cBioPortal data curators when preparing data for upload into the datahub repos.

python-benedict

:blue_book: dict subclass with keylist/keypath support, built-in I/O operations (base64, csv, html, ini, json, pickle, plist, query-string, toml, xls, xml, yaml), s3 support and many utilities.

EthSEQ

Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data