jdiez

QC3

QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.

PyOP2

Framework for performance-portable parallel computations on unstructured meshes

TaarifaAPI

A REST API for the Taarifa platform handling services and resources

pysamstats

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

bedtools-protocols

bwtool

A tool for bigWig files.

cnvkit

Copy number variant detection from targeted DNA sequencing

guacamole-client

The Guacamole project is now Apache Guacamole (http://guacamole.apache.org/). This repository has been repurposed as the base for the Apache Guacamole packages built for Glyptodon Enterprise.

djangotoolbox

Django tools for building nonrel backends

mongodb-engine

Django MongoDB Backend

arrow

🏹 Better dates & times for Python

snake-charmer

A self-contained Python workbench for scientific programming, data mining, maths, stats and visualization

redis-limpyd-jobs

A queue/jobs system based on redis-limpyd, a redis orm (sort of) in python

t-digest

A new data structure for accurate on-line accumulation of rank-based statistics such as quantiles and trimmed means

standalone

The standalone version of Scholar Ninja (exposes API) using node-webkit

bundlewrap

Config management with Python

shiny

Easy interactive web applications with R

docopt

Create *beautiful* command-line interfaces with Python

percol

adds flavor of interactive filtering to the traditional pipe concept of UNIX shell

matchclips2

paired end distance, split reads matching, read depth are used to detect and precisely locate structure variations

rsicnv

Detect copy number variations based on read depth of whole genome sequencing

nextclip

Nextera Long Mate Pair analysis and processing tool

epipy

Python tools for epidemiology

paramiko

The leading native Python SSHv2 protocol library.

pyston_v1

The previous version of Pyston, a faster implementation of the Python programming language. Please use this link for the new repository:

eve

REST API framework designed for human beings

ipython

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

tigra-sv

bam-readcount

Count bases in BAM/CRAM files

sciclone

An R package for inferring the subclonal architecture of tumors