Repositories list

• RMeDPower2

  Public
  Helping design and analyses of data from repeated measures experiments

  HTML

  •0•1•0•0•Updated Aug 13, 2025Aug 13, 2025

• LODopt

  Public
  R package for cell type abundance association analysis for single cell data.

  single-cellglmmassociation-analysis+ 2abundancecelltype-composition

  R

  •0•3•0•0•Updated Aug 12, 2025Aug 12, 2025

• GB_LZ_1373_Transplantation_of_V2as_Manuscript

  Public
  Code for analysis of single-cell/nuclei RNA-seq data in the Transplantation of V2as Manuscript (with Lana Zholudeva et al.)

  R

  •

  MIT License

  •0•0•0•0•Updated Aug 8, 2025Aug 8, 2025

• supremo_lite

  Public
  A lightweight memory first implementation of SuPreMo

  Python

  •

  MIT License

  •0•0•5•0•Updated Aug 4, 2025Aug 4, 2025

• clustOpt

  Public
  Optimizing the resolution parameter for Seurat's FindClusters

  R

  •

  Other

  •1•2•2•0•Updated Aug 1, 2025Aug 1, 2025

• rankSummaries

  Public
  code for the rankSummary analysis. Used for Morris Water Maze analyses

  R

  •0•1•0•0•Updated Jul 22, 2025Jul 22, 2025

• plotly-heatmap2svg

  Public
  Takes an HTML export of a plotly heatmap and outputs a direct PDF and SVG, plus a vectorized SVG of the heatmap cells

  JavaScript

  •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

• Incorporating_pathway_into_DNN

  Public
  Python

  •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

• bioinformatics-promocodes

  Public
  Tool to disseminate promo codes for Bioinformatics Training Program

  JavaScript

  •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

• Interactive-Enrichment-Analysis

  Public
  A set of Shiny apps to provide interactive enrichment analysis and exploration of results.

  bioinformaticsshinyfoss+ 2openscienceenrichment-analysis

  R

  •8•30•12•0•Updated Jul 15, 2025Jul 15, 2025

• bioinformatics-participation

  Public
  For certificates of participation in Bioinformatics Workshops

  JavaScript

  •0•0•0•0•Updated Jul 9, 2025Jul 9, 2025

• MultiONet

  Public
  HTML

  •0•0•0•0•Updated Jun 19, 2025Jun 19, 2025

• Bioinformatics-Workshops

  Public
  Workshops presented by the Gladstone Bioinformatics Core

  HTML

  •76•235•13•0•Updated May 14, 2025May 14, 2025

• scRNA-seq_shiny_app_dashboard

  Public
  R

  •

  MIT License

  •0•1•0•0•Updated Nov 6, 2024Nov 6, 2024

• r_docker

  Public
  Docker container for genomics analyses in R.

  R

  •

  MIT License

  •9•0•0•0•Updated Dec 13, 2023Dec 13, 2023

• C3_R_Bootcamp_Bonus_Day

  Public
  Slides and materials for the last day of the C3 R bootcamp with topics chosen by the students

  CSS

  •0•0•0•0•Updated Nov 9, 2023Nov 9, 2023

• YH_MN01_NatureNeuroscience_paper

  Public
  single-nucleus RNA-seq analysis (15 samples)

  R

  •

  MIT License

  •0•0•1•0•Updated Sep 21, 2023Sep 21, 2023

• annotate-genes

  Public
  Filter GO annotations for a list of genes using mygene.info via R

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 15, 2023Sep 15, 2023

• RMeDPower

  Public
  R

  •0•1•0•0•Updated Aug 14, 2023Aug 14, 2023

• AlleleAnalyzer_bcft_RT

  Public
  A software tool for personalized and allele-specific CRISPR editing.

  Jupyter Notebook

  •

  MIT License

  •5•0•0•0•Updated Jan 3, 2023Jan 3, 2023

• PFOCRInPathwayAnalyses

  Public
  R

  •3•1•0•0•Updated Nov 22, 2021Nov 22, 2021

• Hota_et_al_2021_Brm_safeguards_canalization_cardiac_diff

  Public
  Shell

  •0•0•0•0•Updated Aug 6, 2021Aug 6, 2021

• GB-JL-1189-Jeremy-GEDI

  Public
  GEDI value cutoff threshold estimation

  HTML

  •0•0•0•0•Updated May 28, 2021May 28, 2021

• UCSCbrowserPy

  Public
  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 2, 2021Feb 2, 2021

• wynton-tutorials

  Public
  Legacy wynton documentation for reference

  JavaScript

  •1•0•0•0•Updated Nov 2, 2020Nov 2, 2020

• BC-TM-1123-KC

  Public
  Tamer Mohammed | scRNA-seq

  R

  •0•0•0•0•Updated Jun 18, 2020Jun 18, 2020

• MDC-971-KC

  Public
  HPV type identification

  Shell

  •0•0•0•0•Updated Jun 12, 2020Jun 12, 2020

• scRNA-seq_shiny_app

  Public
  R Shiny application for scRNA-seq

  R

  •0•1•0•0•Updated Apr 30, 2020Apr 30, 2020

• BC-AM-1148

  Public
  R Shiny application for scRNA-seq

  R

  •

  Apache License 2.0

  •1•0•0•0•Updated Mar 18, 2020Mar 18, 2020

• bioinformatics-r-functions

  Public
  Collection of generally useful R functions

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 1, 2020Mar 1, 2020