GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

NCBI Prokaryotic Genome Annotation Pipeline

Open source code for AlphaFold.

snakemake pipeline for creating trees from sequence sets

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

Data visualisation web components for the life sciences.

A package management tools for R

The uncompromising Python code formatter

Integrated Differential Expression and Pathway analysis

Git repository for FASTA36 sequence comparison software

gatk4 RNA variant calling pipeline

Scalable high-throughput short-read open reading frame prediction

Code and tutorials to visualise your data that is both beautiful *and* statistically valid

Phylogenetic orthology inference for comparative genomics

integrated RNA-seq Analysis Pipeline

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the …

⚗️ Simple cloning simulator (Golden Gate etc.) for single and combinatorial assemblies

👁️ Python library to plot DNA sequence features (e.g. from Genbank files)

Automatically exported from code.google.com/p/cdhit

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

Bioinformatics one liners from Ming Tang

A curated list of nextflow based pipelines

Project Manager for NGS data analysis

Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding regions

GATK RNA-Seq Variant Calling in Nextflow

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file form…

RNAseq analysis notes from Ming Tang

WinGet is the Windows Package Manager. This project includes a CLI (Command Line Interface), PowerShell modules, and a COM (Component Object Model) API (Application Programming Interface).