JohnMCMa

Bio-Tools-Primer3Redux

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

asap_to_kite

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

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