Repositories list

• allen-inst-metadata-capture

  Public
  Allen Institute metadata capture system.

  Python

  •22 forks•00 stars•00 issues•00 pull requests•Updated May 3, 2026May 3, 2026

• LFF_spatial_ERC

  Public
  LFF_spatial_ERC

  HTML

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated May 1, 2026May 1, 2026

• LFF_spatial_LC

  Public
  LFF project, spatial_LC data analysis

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• Posit_Connect_shiny_apps

  Public
  Code for Posit Connect R shiny apps (spatialLIBD, iSEE, ...)

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 27, 2026Apr 27, 2026

• spatialDLPFC_SCZ

  Public
  Visium-IF/RNAscope-IF project looking at spatial gene expression in the context of perineuronal nets in DLPFC of neurotypical control donors and donors with a d…

  HTML

  •00 forks•11 star•1616 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• jhpce_module_config

  Public
  JHPCE module configuration files

  Lua

  •00 forks•44 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• jhpce_module_source

  Public
  JHPCE module source files

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• LFF_xenium_LC

  Public
  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• bdportal

  Public
  Brain data portal at LIBD. Not only brain data.

  JavaScript

  •00 forks•00 stars•22 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• spatial_NAc

  Public
  Paired snRNA-seq/Visium for human NAc

  HTML

  •00 forks•00 stars•11 issue•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• DeconvoBuddies

  Public
  Helper Functions for LIBD Deconvolution

  rstatsbioconductordeconvolution

  rstatsbioconductordeconvolution

  R

  •

  Artistic License 2.0

  •33 forks•88 stars•77 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• slurmjobs

  Public
  Helper functions for working with SLURM from R

  slurmrstats

  slurmrstats

  R

  •11 fork•22 stars•22 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• spatialdACC

  Public
  spatialdACC project

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 3, 2026Apr 3, 2026

• visiumStitched

  Public
  R package containing functions useful for stitching Visium capture areas. Related to the example human brain data described at http://research.libd.org/visiumSt…

  rstatsbioconductor10xgenomics+ 4

  rstatsbioconductor10xgenomicsspatial-transcriptomicsvisiumspatiallibdspatialexperiment

  R

  •00 forks•44 stars•22 issues•00 pull requests•Updated Apr 1, 2026Apr 1, 2026

• recount3

  Public
  Explore and download data from the recount3 project

  countgener+ 12

  countgenerhumanmouserstatsbioconductorrnaseqilluminaexon+ 5

  R

  •

  Artistic License 2.0

  •55 forks•3838 stars•2020 issues•00 pull requests•Updated Apr 1, 2026Apr 1, 2026

• TREG

  Public
  Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

  rstatsbioconductorscrna-seq+ 5

  rstatsbioconductorscrna-seqdeconvolutionsnrna-seqrnascopesmfishtreg

  R

  •11 fork•55 stars•22 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• qsvaR

  Public
  Quality Surrogate Variable Analysis for Degradation Correction

  humanrstatsbioconductor+ 3

  humanrstatsbioconductorbraindegradationqsva

  R

  •22 forks•00 stars•1515 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• smokingMouse

  Public
  Provides access to smokingMouse project raw and processed data objects

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• jaffelab

  Public
  R package with commonly used functions by the Jaffe lab

  rstatsrnaseqlibd

  rstatsrnaseqlibd

  R

  •33 forks•88 stars•44 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• megadepth

  Public
  R interface to megadepth: BigWig and BAM related utilities

  rstatsbigwigbam+ 4

  rstatsbigwigbamrecount2megadepthrecount3daspter

  R

  •33 forks•1414 stars•66 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• recountWorkflow

  Public
  Public repo for the recount Bioconductor workflow that is visible at http://bioconductor.org/help/workflows/

  countgener+ 11

  countgenerhumanrstatsbioconductorrnaseqdeseq2illuminaexon+ 4

  TeX

  •00 forks•44 stars•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• GenomicState

  Public
  Build and access GenomicState objects for use with derfinder tools from sources like Gencode

  rstatsderfinderderfinderplot+ 1

  rstatsderfinderderfinderplotgenomicstate

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• spatialLIBD

  Public
  Code for the spatialLIBD R/Bioconductor package and shiny app

  shinyrstatsbioconductor+ 6

  shinyrstatsbioconductorgolem10xgenomicsspatial-transcriptomicsvisiumspatiallibdspatialexperiment

  R

  •

  Artistic License 2.0

  •2222 forks•112112 stars•2626 issues•11 pull request•Updated Mar 27, 2026Mar 27, 2026

• 10xPilot_snRNAseq-human

  Public
  10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC

  HTML

  •

  Artistic License 2.0

  •1010 forks•2525 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• HumanPilot

  Public
  Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

  analysishumanrstats+ 6

  analysishumanrstatsbiorxivbrain10xgenomicsspatial-transcriptomicsvisiumdlpfc

  HTML

  •

  Artistic License 2.0

  •2929 forks•9494 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• spatialDLPFC

  Public
  spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

  rstatsbioconductortranscriptomics+ 5

  rstatsbioconductortranscriptomicsspatial-transcriptomicsvisiumdlpfcspatialdlpfcvisium-spg

  HTML

  •

  Artistic License 2.0

  •66 forks•3131 stars•11 issue•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• spatialDLPFC_SCZ_XENIUM

  Public
  spatialDLPFC_SCZ_XENIUM

  R

  •00 forks•11 star•11 issue•00 pull requests•Updated Mar 20, 2026Mar 20, 2026

• globus

  Public
  LIBD Globus Share Endpoints

  HTML

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 2, 2026Mar 2, 2026

• spatial_HYP

  Public
  HTML

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 16, 2026Feb 16, 2026

• Habenula_Pilot

  Public
  habenulaPilot project code repository

  rna-seqschizophreniabulk-rna-seq+ 2

  rna-seqschizophreniabulk-rna-seqsnrna-seqhabenula

  HTML

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 27, 2026Jan 27, 2026