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bagelp

Parallel version of bagel https://sourceforge.net/projects/bagel-for-knockout-screens/

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

bpipe

cgp_seq_input_val

Sequence data and manifest validation code.

cgpbpipe

local repo of bpipe that handles LSF array jobs

cnvkit

Copy number variant detection from targeted DNA sequencing

consul

Consul is a distributed, highly available, and data center aware solution to connect and configure applications across dynamic, distributed infrastructure.

copynumber

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/copynumber.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=copynumber.

crisprcleanr

Unsupervised correction of gene independent cell responses to CRISPR-cas9

debrowser

Differential Count Data Analysis Toolbox

deepsnv

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/deepSNV.html Contributions: http://github.com/mg14/deepSNV. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=deepSNV.

demo-terraform-101

Before and after demo code for the Terraform Introduction training course

dnacopyp

Runs parallel version of DNAcopy CBS step

docker-images

Repository of Docker images created by Continuum Analytics

encore

Repository to put encore related analysis scripts

irap

integrated RNA-seq Analysis Pipeline

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

mybiotools

ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019 - adapted to run at the Wellcome Sanger Institute

nomad

Nomad is a flexible, enterprise-grade cluster scheduler designed to easily integrate into existing workflows. Nomad can run a diverse workload of micro-service, batch, containerized and non-containerized applications. Nomad is easy to operate and scale and integrates seamlessly with Consul and Vault.

packer

Packer is a tool for creating identical machine images for multiple platforms from a single source configuration.

pcap-core

NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)

peakrescue

peakrescue-1

Method to rescue ambiguous reads in RNA-Seq experiments

resops_workshop_portal_cluster

s3cmd-plugin

Dockstore S3cmd file provisioning plugin

tabix

Note: tabix and bgzip binaries are now part of the HTSlib project.

user_guide

The CWL v1.0 user guide

vagrant

Vagrant is a tool for building and distributing development environments.

vault

A tool for secrets management, encryption as a service, and privileged access management