helrick

savana

Somatic structural variant caller for long-read data

phosx

Kinase activity inference from phosphosproteomics data

CATD_snakemake

Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq datasets

SComatic

A tool for detecting somatic variants in single cell data

BOSS-RUNS

Dynamic, adaptive sampling during nanopore sequencing

ggcoverage

Visualize and annotate genomic coverage with ggplot2

telomere_fusions

Code to call telomere fusions using DNA sequencing data

ReConPlot

colord

A versatile compressor of third generation sequencing reads.

useful-sed

Useful sed scripts & patterns.

RISE

RISE: "Live" Reveal.js Jupyter/IPython Slideshow Extension

remote-pbcopy-iterm2

remote pbcopy for iTerm2

Made-With-ML

Learn how to design, develop, deploy and iterate on production-grade ML applications.

seq

A high-performance, Pythonic language for bioinformatics

MoMI-G

Modular Multi-scale Integrated Genome Graph Browser

elsapy

A Python module for use with Elsevier's APIs: Scopus, ScienceDirect, others.

svtools

Tools for processing and analyzing structural variants.

SVAFotate

reticulatus

A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads

jigv

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

oneliners

Useful bash one-liners for bioinformatics.

htslib

C library for high-throughput sequencing data formats

mavis

Merging, Annotation, Validation, and Illustration of Structural variants

octopus

Bayesian haplotype-based mutation calling

singularity-deploy

Build and deploy Singularity containers to GitHub releases, and pull with the singularity-hpc client

singularity-hpc

Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.

JaBbA

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.

wfpm

WorkFlow Package Manager

feedparser

Parse feeds in Python

CoolBox

Jupyter notebook based genomic data visualization toolkit.