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adam

A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

aoc2021

assotester

R package AssotesteR

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

az_test

basejump

Base functions for bioinformatics and R package development.

bcbio-conda

conda recipes for bcbio python code and dependencies

bcbio-nextgen

Best-practice pipelines for fully automated high throughput sequencing analysis

bcbio-nextgen-test-data

Unit test data for bcbio-nextgen

bcbio-test-data

bcbio.rnaseq

Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway analysis for bcbio RNA-seq runs

bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure

bcbio.variation.recall

Parallel merging, squaring off and ensemble calling for genomic variants

bcbio_docker

Automated Docker builds for bcbio

bcbio_repenrich2

Prepares samples and runs RepEnrich2 from a bcbio-nextgen RNA-seq run

bcbio_validations

Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses

bcbiobase

Base functions and generics for bcbio R packages.

bcbiornaseq

Quality control and differential expression for bcbio RNA-seq experiments.

bcbiosinglecell

Utility functions for analysis of bcbio-nextgen single-cell RNA-seq data.

bik-manipulation

Training set of manipulated images from open access publications identified by Elisabeth Bik

bioconda-recipes

Conda recipes for the bioconda channel.

bioconda-utils

Utilities for building and managing bioconda recipes

biod

Bioinformatics library in D. (utils for working with SAM, BAM, SFF formats)

bipy

DEPRECATED Lightweight bioinformatics pipeline tools using iPython

breakseq2

BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants

brew-ds

Common Data Science set up for Mac 🍺🔬

brushback

Does brushing back a batter help a pitcher on subsequent pitches to the outside of the plate?

chainfiles

Chain files for use with liftOver and CrossMap

chanjo

Chanjo provides a better way to analyze coverage data in clinical sequencing.

chipseq-greylist

Python implementation of the GreyListChIP Bioconductor package