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gradle-signing-bug

Small reproduction of a gradle bug

grgit

The Groovy way to use Git.

hadoop-bam

Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework

homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew and Linuxbrew package managers

homebrew-core

🍻 Default formulae for the missing package manager for macOS

homebrew-louis

A personal homebrew tap

homebrew-science

:microscope: Scientific formulae for the Homebrew package manager

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http-nio

**Under development** HTTP/S FileSystem provider for Java NIO.2

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

java-storage

java-storage-nio

jenv

Manage your Java environment

jopt-simple

Java library for parsing command line options

jstack-profiler

Simple java profiler that take jstack output as input

lunaris

maftools

Python convenience functions for working with mutation annotation format files (MAF)

maven-badges

A node.js implementation of https://github.com/jirutka/maven-badges, originally created in ruby.

misc

miscellaneous scripts

mutect

MuTect -- Accurate and sensitive cancer mutation detection

my-new-project

test project

nucleus

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

optparse

R package proving commandline optional argument parser

panelofnormalsfilter

Filtering a somatic variant file against a panel of normal variants.

pipelines

Pipelines for processing malaria parasite and mosquito genome sequence data.

plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.

practice

pytables

PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data.

renjin-docs

Documentation for Renjin, the R interpreter for the JVM