Repositories list

• globus

  Public
  LIBD Globus Share Endpoints

  HTML

  •1•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• jhpce_module_source

  Public
  JHPCE module source files

  Shell

  •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

• jhpce_module_config

  Public
  JHPCE module configuration files

  Lua

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

• spatialdACC

  Public
  spatialdACC project

  HTML

  •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• DeconvoBuddies

  Public
  Helper Functions for LIBD Deconvolution

  rstatsbioconductordeconvolution

  R

  •

  Artistic License 2.0

  •2•5•7•0•Updated Jul 28, 2025Jul 28, 2025

• spatial_hpc

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

  HTML

  •1•6•1•0•Updated Jul 25, 2025Jul 25, 2025

• Habenula_Pilot

  Public
  habenulaPilot project code repository

  rna-seqschizophreniabulk-rna-seq+ 2snrna-seqhabenula

  HTML

  •1•0•0•0•Updated Jul 21, 2025Jul 21, 2025

• smoking-nicotine-mouse

  Public
  Smoking mouse project

  R

  •0•1•1•0•Updated May 31, 2025May 31, 2025

• BiocMAP

  Public
  Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow

  nextflowwgbs

  HTML

  •1•3•4•0•Updated May 27, 2025May 27, 2025

• BLA_crossSpecies

  Public
  Collaboration between Costa, Martinowich, and Hicks labs investigating basolateral amygdala cell-types across huamn and non-human primate species.

  R

  •0•3•10•0•Updated May 16, 2025May 16, 2025

• recount3

  Public
  Explore and download data from the recount3 project

  countgener+ 12humanmouserstatsbioconductorrnaseqilluminaexon+ 5

  R

  •4•36•20•0•Updated May 15, 2025May 15, 2025

• spatialLIBD

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

  shinyrstatsbioconductor+ 6golem10xgenomicsspatial-transcriptomicsvisiumspatiallibdspatialexperiment

  R

  •23•96•23•1•Updated May 9, 2025May 9, 2025

• spatial_HYP

  Public
  HTML

  •0•0•0•0•Updated Apr 30, 2025Apr 30, 2025

• LIBD_VA_PTSD_RNAseq_4Region

  Public
  R

  •0•3•0•0•Updated Apr 14, 2025Apr 14, 2025

• spatial_DG_lifespan

  Public
  Spatial transcriptomics (Visium) in dentate gyrus of hippocampus over the lifespan

  HTML

  •0•0•0•0•Updated Apr 4, 2025Apr 4, 2025

• DLPFC_snRNAseq

  Public
  snRNA_seq portion of the spatialDLPFC project

  rstatsbioconductorsnrna-seq+ 1spatialdlpfc

  HTML

  •1•6•0•0•Updated Mar 14, 2025Mar 14, 2025

• Posit_Connect_shiny_apps

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

  R

  •0•0•0•0•Updated Mar 14, 2025Mar 14, 2025

• goesHyde_mdd_rnaseq

  Public
  Fernando Goes and Thomas Hyde MDD RNA-seq project

  HTML

  •0•2•7•0•Updated Mar 12, 2025Mar 12, 2025

• SPEAQeasy

  Public
  SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.

  pipelinerstatsrnaseq+ 4hisat2speaqeasynextflowrna-seq-pipeline

  HTML

  •

  MIT License

  •4•6•21•0•Updated Mar 11, 2025Mar 11, 2025

• Human_DLPFC_Deconvolution

  Public
  Roff

  •

  MIT License

  •0•3•0•0•Updated Mar 11, 2025Mar 11, 2025

• spatialDLPFC_Visium_Sp09_pseudobulk-

  Public
  Testing GitHub and Posit Connect integration using spatialDLPFC files

  R

  •0•0•0•0•Updated Feb 28, 2025Feb 28, 2025

• spatialDLPFC

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

  rstatsbioconductortranscriptomics+ 5spatial-transcriptomicsvisiumdlpfcspatialdlpfcvisium-spg

  HTML

  •4•22•0•0•Updated Feb 19, 2025Feb 19, 2025

• slurmjobs

  Public
  Helper functions for working with SLURM from R

  slurmrstats

  R

  •1•2•2•0•Updated Feb 4, 2025Feb 4, 2025

• 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/visiumStitched_brain/.

  rstatsbioconductor10xgenomics+ 4spatial-transcriptomicsvisiumspatiallibdspatialexperiment

  R

  •0•4•2•0•Updated Jan 3, 2025Jan 3, 2025

• recount3-docs

  Public
  Documentation for all things related to `recount3`

  humanmouserstats+ 7bioconductorrnaseqrecounthg38recount2mm10recount3

  R

  •1•2•0•0•Updated Dec 13, 2024Dec 13, 2024

• GenomicState

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

  rstatsderfinderderfinderplot+ 1genomicstate

  R

  •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• jaffelab

  Public
  R package with commonly used functions by the Jaffe lab

  rstatsrnaseqlibd

  R

  •3•7•4•0•Updated Dec 12, 2024Dec 12, 2024

• megadepth

  Public
  R interface to megadepth: BigWig and BAM related utilities

  rstatsbigwigbam+ 4recount2megadepthrecount3daspter

  R

  •2•12•6•0•Updated Dec 12, 2024Dec 12, 2024

• SPEAQeasy-example

  Public
  Full length example for SPEAQeasy

  rstatsrnaseqspeaqeasy

  Shell

  •0•1•0•0•Updated Dec 11, 2024Dec 11, 2024

• recountWorkflow

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

  countgener+ 11humanrstatsrnaseqdeseq2illuminaexonjunction+ 4

  TeX

  •0•4•0•0•Updated Dec 10, 2024Dec 10, 2024