Stars
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.
Integrated Differential Expression and Pathway analysis
Git repository for FASTA36 sequence comparison software
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
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
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).