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apptainer

Apptainer: Application containers for Linux

arboreto

A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.

archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

biofx_python

Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)

biomedical-knowledge-mining-book

:books: Biomedical knowledge mining using GOSemSim and clusterProfiler

cactus_alignments_tools

The toolbox used to deal with cactus whole genome alignments

cccexplorer

Paper - Transcriptome analysis of individual stromal cell populations identifies stroma-tumor crosstalk in mouse lung cancer model

celescope

Single Cell Analysis Pipelines

cellhint

A tool for semi-automatic cell type harmonization and integration

cheatsheets

Posit Cheat Sheets - Can also be found at https://posit.co/resources/cheatsheets/.

chemdfm

chm13

The complete sequence of a human genome

cnvkit

Copy number variant detection from targeted DNA sequencing

complexheatmap

Make Complex Heatmaps

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

ensembl-funcgen

Ensembl Funcgen Perl API and SQL schema

genie3

Machine learning-based approach for the inference of gene regulatory networks from expression data.

genome-stratifications

Stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team

genomescope2.0

Reference-free profiling of polyploid genomes

hap.py

Haplotype VCF comparison tools

megatron-lm

Ongoing research training transformer models at scale

meryl

A genomic k-mer counter (and sequence utility) with nice features.

monocle-release

nichenetr

NicheNet: predict active ligand-target links between interacting cells

nrnb.github.io

website code for the national resource for network biology

omnipathr

R client for the OmniPath web service

phd-thesis

I am in [research] stepped in so far that, should I wade no more, Returning were as tedious as go o'er. -MacBeth

pydnase

Python module for the easy handling and analysis of DNase-seq data

pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

pyxis

Container plugin for Slurm Workload Manager