Repositories list

• nf_xpatial

  Public
  nf_xpatial is a best-practices workflow for QC, normalization, integration, clustering and visualization

  spatial-transcriptomicsxenium

  spatial-transcriptomicsxenium

  R

  •

  GNU General Public License v3.0

  •00 forks in U-BDS/nf_xpatial•33 stars in U-BDS/nf_xpatial•1212 issues in U-BDS/nf_xpatial•00 pull requests in U-BDS/nf_xpatial•Updated Oct 16, 2026Oct 16, 2026

• 2026-10-22-uab

  Public
  HTML

  •

  Other

  •00 forks in U-BDS/2026-10-22-uab•00 stars in U-BDS/2026-10-22-uab•00 issues in U-BDS/2026-10-22-uab•00 pull requests in U-BDS/2026-10-22-uab•Updated Oct 15, 2026Oct 15, 2026

• nf_xpatial_paper

  Public
  R

  •00 forks in U-BDS/nf_xpatial_paper•00 stars in U-BDS/nf_xpatial_paper•00 issues in U-BDS/nf_xpatial_paper•00 pull requests in U-BDS/nf_xpatial_paper•Updated Aug 21, 2026Aug 21, 2026

• scnanoseq_analysis

  Public
  nf-corescnanoseq

  nf-corescnanoseq

  R

  •00 forks in U-BDS/scnanoseq_analysis•11 star in U-BDS/scnanoseq_analysis•00 issues in U-BDS/scnanoseq_analysis•00 pull requests in U-BDS/scnanoseq_analysis•Updated Aug 21, 2026Aug 21, 2026

• test-datasets

  Public
  Test data to be used for automated testing with the nf-core pipelines

  nf-core

  nf-core

  MIT License

  •541541 forks in U-BDS/test-datasets•00 stars in U-BDS/test-datasets•00 issues in U-BDS/test-datasets•00 pull requests in U-BDS/test-datasets•Updated Aug 19, 2026Aug 19, 2026

• scnanoseq

  Public
  Single-cell/nuclei pipeline for data derived from Oxford Nanopore

  single-celloxford-nanoporenf-core

  single-celloxford-nanoporenf-core

  Nextflow

  •

  MIT License

  •2121 forks in U-BDS/scnanoseq•11 star in U-BDS/scnanoseq•00 issues in U-BDS/scnanoseq•33 pull requests in U-BDS/scnanoseq•Updated Jul 21, 2026Jul 21, 2026

• training_guides

  Public
  Compilation of training guides

  dockerrstudiosingularity+ 2

  dockerrstudiosingularitydata-analysisnf-core

  Shell

  •11 fork in U-BDS/training_guides•55 stars in U-BDS/training_guides•11 issue in U-BDS/training_guides•00 pull requests in U-BDS/training_guides•Updated Jul 20, 2026Jul 20, 2026

• configs

  Public
  Config files used to define parameters specific to compute environments at different Institutions

  Nextflow

  •

  MIT License

  •376376 forks in U-BDS/configs•00 stars in U-BDS/configs•00 issues in U-BDS/configs•00 pull requests in U-BDS/configs•Updated Mar 19, 2026Mar 19, 2026

• 2026-01-29-uab

  Public
  HTML

  •

  Other

  •00 forks in U-BDS/2026-01-29-uab•00 stars in U-BDS/2026-01-29-uab•00 issues in U-BDS/2026-01-29-uab•00 pull requests in U-BDS/2026-01-29-uab•Updated Feb 2, 2026Feb 2, 2026

• nf-core_workshop

  Public
  Training materials which introduces nf-core with a demostration of nf-core/rnaseq, custom profiling and Seqera AI

  nextflownf-coreseqera

  nextflownf-coreseqera

  Shell

  •

  GNU General Public License v3.0

  •00 forks in U-BDS/nf-core_workshop•00 stars in U-BDS/nf-core_workshop•00 issues in U-BDS/nf-core_workshop•00 pull requests in U-BDS/nf-core_workshop•Updated Sep 22, 2025Sep 22, 2025

• 2025-07-09-uab

  Public
  Workshop website for Git, Bash, and Python carpentry workshop hosted by U-BDS for July 9th, 2025 - July 10th, 2025

  HTML

  •

  Other

  •00 forks in U-BDS/2025-07-09-uab•00 stars in U-BDS/2025-07-09-uab•00 issues in U-BDS/2025-07-09-uab•00 pull requests in U-BDS/2025-07-09-uab•Updated Jul 24, 2025Jul 24, 2025

• bulk_RNA_seq_workshop

  Public
  Workshop materials for the U-BDS bulk RNA-seq lessons

  workshopbulk-rna-seq

  workshopbulk-rna-seq

  R

  •

  GNU General Public License v3.0

  •44 forks in U-BDS/bulk_RNA_seq_workshop•11 star in U-BDS/bulk_RNA_seq_workshop•00 issues in U-BDS/bulk_RNA_seq_workshop•00 pull requests in U-BDS/bulk_RNA_seq_workshop•Updated May 28, 2025May 28, 2025

• 2024-07-09-uab

  Public
  00 forks in U-BDS/2024-07-09-uab•00 stars in U-BDS/2024-07-09-uab•00 issues in U-BDS/2024-07-09-uab•00 pull requests in U-BDS/2024-07-09-uab•Updated Jul 5, 2024Jul 5, 2024

• .github

  Public
  The UAB Biological Data Science Core (U-BDS) is a UAB institutional resource which aims provide services, foster long-term collaborations with the UAB research …

  11 fork in U-BDS/.github•00 stars in U-BDS/.github•00 issues in U-BDS/.github•00 pull requests in U-BDS/.github•Updated Apr 29, 2024Apr 29, 2024

• 2024-03-18-uab

  Public template
  workshop

  workshop

  HTML

  •

  Other

  •534534 forks in U-BDS/2024-03-18-uab•00 stars in U-BDS/2024-03-18-uab•00 issues in U-BDS/2024-03-18-uab•00 pull requests in U-BDS/2024-03-18-uab•Updated Mar 14, 2024Mar 14, 2024

• git-novice

  Public
  Version Control with Git

  workshop

  workshop

  Other

  •973973 forks in U-BDS/git-novice•00 stars in U-BDS/git-novice•00 issues in U-BDS/git-novice•00 pull requests in U-BDS/git-novice•Updated Feb 5, 2024Feb 5, 2024

• 2023-12-14-uab

  Public
  A repository hosting the website for UAB's Fall 2023 Software Carpentry Workshop.

  rworkshopswc+ 3

  rworkshopswcsoftware-carpentryuabubds

  HTML

  •

  Other

  •00 forks in U-BDS/2023-12-14-uab•11 star in U-BDS/2023-12-14-uab•11 issue in U-BDS/2023-12-14-uab•00 pull requests in U-BDS/2023-12-14-uab•Updated Dec 15, 2023Dec 15, 2023

• zebrafish_telencephalon_atlas

  Public
  A R Shiny app of the transcriptome atlas of the maturing zebrafish telencephalon

  rshiny

  rshiny

  R

  •

  MIT License

  •00 forks in U-BDS/zebrafish_telencephalon_atlas•00 stars in U-BDS/zebrafish_telencephalon_atlas•00 issues in U-BDS/zebrafish_telencephalon_atlas•00 pull requests in U-BDS/zebrafish_telencephalon_atlas•Updated Jul 26, 2023Jul 26, 2023

• GbmPdxSTR

  Public
  Source code for the GbmPdxSTR app available at gliomamodels.com

  rshiny

  rshiny

  R

  •

  Other

  •00 forks in U-BDS/GbmPdxSTR•00 stars in U-BDS/GbmPdxSTR•00 issues in U-BDS/GbmPdxSTR•00 pull requests in U-BDS/GbmPdxSTR•Updated Mar 27, 2023Mar 27, 2023

• containers

  Public
  Bioinformatics containers

  Dockerfile

  •

  Apache License 2.0

  •266266 forks in U-BDS/containers•00 stars in U-BDS/containers•00 issues in U-BDS/containers•00 pull requests in U-BDS/containers•Updated Feb 24, 2023Feb 24, 2023

• multi-package-containers

  Public
  Testing building mulled containers for multi-requirement tools.

  246246 forks in U-BDS/multi-package-containers•00 stars in U-BDS/multi-package-containers•00 issues in U-BDS/multi-package-containers•00 pull requests in U-BDS/multi-package-containers•Updated Feb 22, 2023Feb 22, 2023

• mulled

  Public
  Mulled - Automatized Containerized Software Repository

  3838 forks in U-BDS/mulled•00 stars in U-BDS/mulled•00 issues in U-BDS/mulled•00 pull requests in U-BDS/mulled•Updated Feb 10, 2023Feb 10, 2023