Repositories list

• 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 Aug 28, 2026Aug 28, 2026

• LFF_spatial_ERC

  Public
  LFF_spatial_ERC

  HTML

  •

  MIT License

  •00 forks•22 stars•11 issue•00 pull requests•Updated Aug 28, 2026Aug 28, 2026

• spatial_HYP

  Public
  HTML

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 28, 2026Aug 28, 2026

• LFF_spatial_LC

  Public
  LFF project, spatial_LC data analysis

  HTML

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

• spatialAmygdala

  Public
  R

  •00 forks•22 stars•00 issues•00 pull requests•Updated Aug 27, 2026Aug 27, 2026

• LieberInstitute.github.io

  Public
  public website for LIBD content

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 26, 2026Aug 26, 2026

• gwas-pgs-prs

  Public
  Pipeline for preparing GWAS data for polygenic risk score calculation

  R

  •00 forks•11 star•00 issues•11 pull request•Updated Aug 23, 2026Aug 23, 2026

• jhpce_module_config

  Public
  JHPCE module configuration files

  Lua

  •00 forks•44 stars•00 issues•00 pull requests•Updated Aug 18, 2026Aug 18, 2026

• jhpce_module_source

  Public
  JHPCE module source files

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 18, 2026Aug 18, 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•3333 stars•11 issue•00 pull requests•Updated Aug 14, 2026Aug 14, 2026

• spatialdACC

  Public
  spatialdACC project

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 13, 2026Aug 13, 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 Aug 13, 2026Aug 13, 2026

• spatial_hpc

  Public
  Repository for the spatial (U01) hippocampus (hipc) project

  HTML

  •22 forks•99 stars•11 issue•00 pull requests•Updated Aug 13, 2026Aug 13, 2026

• spatial_NAc

  Public
  Paired snRNA-seq/Visium for human NAc

  HTML

  •00 forks•00 stars•11 issue•00 pull requests•Updated Aug 13, 2026Aug 13, 2026

• libdreq

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Aug 7, 2026Aug 7, 2026

• spatialLIBD

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

  shinyrstatsbioconductor+ 6

  shinyrstatsbioconductorgolem10xgenomicsspatial-transcriptomicsvisiumspatiallibdspatialexperiment

  R

  •

  Artistic License 2.0

  •2323 forks•113113 stars•2525 issues•11 pull request•Updated Jul 24, 2026Jul 24, 2026

• smoking-nicotine-mouse

  Public
  Smoking mouse project

  R

  •00 forks•11 star•11 issue•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• LFF_xenium_LC

  Public
  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 21, 2026Jul 21, 2026

• fentanyl_rat_hb_amy

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 15, 2026Jul 15, 2026

• LIBD_VA_PTSD_RNAseq_4Region

  Public
  R

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jun 16, 2026Jun 16, 2026

• mango

  Public
  A suite of agent management UIs, MCPs, skills, hooks, tmux configurations and more to support rigor and productivity in agentic coding, with support for Claude …

  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jun 15, 2026Jun 15, 2026

• globus

  Public
  LIBD Globus Share Endpoints

  HTML

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 15, 2026Jun 15, 2026

• DeconvoBuddies

  Public
  Helper Functions for LIBD Deconvolution

  rstatsbioconductordeconvolution

  rstatsbioconductordeconvolution

  R

  •

  Artistic License 2.0

  •33 forks•1010 stars•88 issues•00 pull requests•Updated Jun 15, 2026Jun 15, 2026

• bdportal

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

  JavaScript

  •00 forks•00 stars•22 issues•00 pull requests•Updated May 28, 2026May 28, 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 May 15, 2026May 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 May 12, 2026May 12, 2026

• spatialDLPFC_SCZ_XENIUM

  Public
  spatialDLPFC_SCZ_XENIUM

  R

  •11 fork•00 stars•22 issues•00 pull requests•Updated May 6, 2026May 6, 2026

• allen-inst-metadata-capture

  Public
  Allen Institute metadata capture system.

  Python

  •22 forks•00 stars•00 issues•00 pull requests•Updated May 4, 2026May 4, 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•4040 stars•2121 issues•00 pull requests•Updated Apr 1, 2026Apr 1, 2026