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asap_to_kite

CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processing

bio-tools-primer3redux

A reimplementation of BioPerl's Primer3-related code for primer3 v1 and v2

biopython

Official git repository for Biopython (converted from CVS)

chromvar

chromatin Variability Across Regions (of the genome!)

copywriter

DNA copy number detection from off-target sequence data

datavis

Using a bubble chart to demonstrate that from a dataset of 1,157 baseball players, right-handed players have lower batteling average and home run counts.

dendextend

Extending R's Dendrogram Functionality

ensembl-vep

The Variant Effect Predictor predicts the functional effects of genomic variants

epic2

Ultraperformant reimplementation of SICER

histonehmm

Differential peak calling tool for ChIP-seq data

hlaminer

HLA predictions from NGS shotgun data

hotspot3d

3D hotspot mutation proximity analysis tool

intermine

A powerful open source data warehouse system

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

mupexi

MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.

nucleus

Python and C++ code for reading and writing genomics data.

optitype

Precision HLA typing from next-generation sequencing data

parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

phaser

phasing and Allele Specific Expression from RNA-seq

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

sc_read_kallisto_wrapper

wrapper for single cell transcriptomics pipeline with kallisto

scito-seq

SCITO-seq related, forked from original code

seurat

R toolkit for single cell genomics

tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data

ud120

vcf_parser

Simple vcf parser, based on PyVCF

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

vep_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)

xenofilter

Filtering of PDX samples for mouse derived reads