https://github.com/bioarchlinux/bioarchlinux-tools
Tools for maintaining BioArchLinux
https://github.com/bioatmosphere/e3sm
Energy Exascale Earth System Model source code. NOTE: use "maint" branches for your work. Head of master is not validated.
https://github.com/bioatmosphere/pytorch-generative
Easy generative modeling in PyTorch.
https://github.com/bioatmosphere/generative-ecosystem-model
GEM: Generative Ecosystem Model
https://github.com/bioatmosphere/uvafmevoc2017
Scripts and Data underlying the 2017 Ecological Modelling paper on UVAFME-VOC.
https://github.com/bioatmosphere/fates
repository for the Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
https://github.com/bioatmosphere/microbiome-climate-gradient
Application of DEMENTpy to a climate gradient in Southern California
https://github.com/biocommons/uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
https://github.com/biocommons/anyvar
[in development] Proof-of-Concept variation translation, validation, and registration service
https://github.com/biocommons/mirrors-ncbi
Makefile (of all things) to space-efficiently mirror selected NCBI resources
https://github.com/biocomputingup/cagi-p16-assessment
https://genomeinterpretation.org/content/predict-how-variants-p16-tumor-suppressor-protein-affect-cell-proliferation
https://github.com/biocomputingup/geometre_results
GeomeTRe calculation results for STRPs from RepeatsDB v4, including large-scale and statistical analyses. Reproducible Jupyter Notebook scripts are available in this repository.
https://github.com/biocomputingup/caid-reference
Critical Assessment of Protein Intrinsic Disorder (CAID) - Reference generation and analysis
https://github.com/biocomputingup/drmaatic
DRMAAtic REST APIs for job scheduling @BioCompUP
https://github.com/biocomputingup/cagi-id-assessment
Assessment scripts for ID challenge of CAGI 5
https://github.com/biocomputingup/proseqviewer-documentation
Reference documentation of ProSeqViewer
https://github.com/biocomputingup/biological_data
Biological Data - Data Science - University of Padova
https://github.com/bioconductor/bsgenome
Software infrastructure for efficient representation of full genomes and their SNPs
https://github.com/bioconductor/rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
https://github.com/bioconductor/ucsc.utils
Low-level utilities to retrieve data from the UCSC Genome Browser
https://github.com/bioconductor/csama-labs
laboratory materials for the Bressanone course
https://github.com/bioconductor/eurobioc2025
Website of the European Bioconductor Conference 2025
https://github.com/bioconductor/s4arrays
Foundation of array-like containers in Bioconductor
https://github.com/bioconductor/hdf5array
HDF5 datasets as array-like objects in R
https://github.com/bioconductor/annotationhub_docker
Docker container for AnnotationHub
https://github.com/bioconductor/csama
Course material for CSAMA: Statistical Data Analysis for Genome Scale Biology
https://github.com/bioconductor/s4vectors
Foundation of vector-like and list-like containers in Bioconductor
https://github.com/bioconductor/anvil
Interact with AnVIL and Leonardo projects
https://github.com/bioconductor/annotationdbi
Manipulation of SQLite-based annotations in Bioconductor
https://github.com/bioconductor/uidaho2017
Talk and Workshop Material for University of Idaho, 2017
https://github.com/bioconductor/code.bioconductor.org
Tools for browsing and searching the code behind Bioconductor packages
https://github.com/bioconductor/seqinfo
A simple S4 class for storing basic information about a collection of genomic sequences
https://github.com/bioconductor/bioc-run
Helper script for bioconductor/bioconductor_docker
https://github.com/bioconductor/annotation
Bioconductor annotation workflow package
https://github.com/bioconductor/biocreporting
Public repo for Bioconductor project reporting 2022
https://github.com/bioconductor/bioc2u
Building containers and holding some code for bioc2u, an attempt at extending r2u to all bioc packages, and provide precompiled binaries for ubuntu systems
https://github.com/bioconductor/hubsingest
Scripts to facilitate ingestion at temporary endpoints for data targeting the Bioconductor Hubs
