pkMyt1

ScarMapper

Method to map double strand break repair scars at defined loci

scp.py

scp module for paramiko

Volundr

Bioinformatics pipeline to analyze CRISPR synthetic lethal and synthetic viable screens

hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

CodeIgniter4

Open Source PHP Framework (originally from EllisLab)

CodeIgniter-Ion-Auth

Simple and Lightweight Auth System for CodeIgniter

wxGlade

wxGlade is a GUI builder written in Python for the GUI toolkit wxWidgets / wxPython. Documentation snapshot: http://wxglade.sourceforge.net/docs/index.html

pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

Connor

Deduplication based on custom inline DNA barcodes.

atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

SnpEff

multiprocess

better multiprocessing and multithreading in Python

dill

serialize all of Python

pathos

parallel graph management and execution in heterogeneous computing

ginkgo

Cloud-based single-cell copy-number variation analysis tool

pydendroheatmap

A tool for generating heatmaps from hierarchically clustered data.

pyGeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

nfsim

A general-purpose, stochastic, biochemical reaction simulator for large reaction networks

Duplex-Sequencing