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2020_population_genetics

acranker

AcRanker is a machine learning system developed in python that ranks proteins in a proteome as per their Anti-CRISPR tendencies predicted using sequence features.

acrfinder

AcrFinder, a tool for automated identification of Acr-Aca loci

archs4

ARCHS4 RNA-seq processing scripts and web server pages.

arteria-packs

StackStorm packs to automate sequencing center operations

autofastq

script to automate Illumina bcl2fastq utility

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

awesome-deepbio

A curated list of awesome deep learning applications in the field of computational biology

badmixture

R package for comparing mixture solutions to similarity data, with a focus STRUCTURE like models to ChromoPainter palettes

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bio-ml

Command lines for the BIO-ML resources

biobambam

Tools for bam file processing

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics

:microscope: Path to a free self-taught education in Bioinformatics!

bioinformatics-toolbox

Docker container for bioinformatics tools and pipelines

bioinformatics-workbook

Bioinformatics Workbook repository

biolab

Bioinformatics Docker Container

e-mtab-6141

Data from Lewis, Barnes, Blighe et al., Cell Rep. 2019 Aug 27; 28(9): 2455–2470.e5.

edgepy

A Python implementation of edgeR for differential expression analysis

egyptref

Scripts and pipelines used in the generation of "An Egyptian Genome Reference"

exomiser

A Tool to Annotate and Prioritize Exome Variants

flexbar

flexible barcode and adapter removal

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

gatk

Official code repository for GATK versions 4 and up

howtos

Manuals and examples

htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

irkernel

R kernel for Jupyter

kent

UCSC Genome Browser source tree. Stable branch: "beta".

kraken2

The second version of the Kraken taxonomic sequence classification system

krona

Interactively explore metagenomes and more from a web browser.