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accuracode

AccuraCode® analysis pipeline

agat

Another Gtf/Gff Analysis Toolkit

bio7

Bio7

biogrid-annotation

Tools for updating and maintaining BioGRID annotation resources for use with a variety of projects.

biojava-tutorial

:book::books:An introductory tutorial for BioJava

bioperl-docker

Docker files for BioPerl

bioperl-live

Core BioPerl 1.x code

bioruby

bioruby

browser

A tool for visualising and interacting with pathways data

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

cath-tools

Protein structure comparison tools such as SSAP and SNAP

cellranger

10x Genomics Single Cell 3' Gene Expression and VDJ Assembly

cellrangerrkit

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

chebi

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.

chinamap

complexheatmap

Make Complex Heatmaps

corrplot

Package corrplot is for visualizing a correlation matrix

cytoscape-admin-scripts

Build and maintenance scripts for Cytoscape core developers.

cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js

deconstructsigs

deconstructSigs

deepmass

DeepMass is a suite of tools to enable mass spectrometry data analysis using modern machine learning techniques.

diffenrich

development of methods and software for differential enrichment analysis

dndscv

dN/dS methods to quantify selection in cancer and somatic evolution

doc-annovar

Documentation for the ANNOVAR software

fireworks

go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.

heat-diffusion

machinelearning

Basic Machine Learning and Deep Learning

manta

Structural variant and indel caller for mapped sequencing data

mtserver_oaat2

MTServer_OAAT of Version 2