Repositories list

• spatialLIBD

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

  shinyrstatsbioconductor+ 6golem10xgenomicsspatial-transcriptomicsvisiumspatiallibdspatialexperiment

  R

  •17•83•24•0•Updated Oct 31, 2024Oct 31, 2024

• DeconvoBuddies

  Public
  Helper Functions for LIBD Deconvolution

  rstatsbioconductordeconvolution

  R

  •1•3•5•0•Updated Oct 31, 2024Oct 31, 2024

• jhpce_module_source

  Public
  JHPCE module source files

  Shell

  •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

• jhpce_module_config

  Public
  JHPCE module configuration files

  Lua

  •0•4•0•0•Updated Oct 29, 2024Oct 29, 2024

• 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•1•2•0•Updated Oct 24, 2024Oct 24, 2024

• BLA_crossSpecies

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

  R

  •0•1•10•0•Updated Oct 23, 2024Oct 23, 2024

• smoking-nicotine-mouse

  Public
  Smoking mouse project

  R

  •0•0•0•0•Updated Oct 21, 2024Oct 21, 2024

• qsvaR

  Public
  Quality Surrogate Variable Analysis for Degradation Correction

  humanrstatsbioconductor+ 3braindegradationqsva

  R

  •2•0•15•0•Updated Oct 9, 2024Oct 9, 2024

• ls_molecular-profiling

  Public
  ls_molecular-profiling

  HTML

  •0•1•0•0•Updated Sep 25, 2024Sep 25, 2024

• spatial_DG_lifespan

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

  HTML

  •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

• slurmjobs

  Public
  Helper functions for working with SLURM from R

  slurmrstats

  R

  •1•2•2•0•Updated Sep 20, 2024Sep 20, 2024

• Kleinman_EatingDisorders_RNASeq

  Public
  R

  •0•2•0•0•Updated Sep 20, 2024Sep 20, 2024

• globus

  Public
  LIBD Globus Share Endpoints

  HTML

  •1•0•0•0•Updated Sep 16, 2024Sep 16, 2024

• spatial_hpc

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

  HTML

  •0•1•1•0•Updated Sep 11, 2024Sep 11, 2024

• visiumStitched_brain

  Public
  Example human brain data used for https://research.libd.org/visiumStitched/.

  spatialrstatsbioconductor+ 4transcriptomicsvisiumspatiallibdvisiumstitched

  HTML

  •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

• ANCR

  Public
  Scripts for "Network-wide risk convergence in gene co-expression identifies reproducible genetic hubs of schizophrenia risk"

  R

  •0•0•0•0•Updated Sep 4, 2024Sep 4, 2024

• goesHyde_mdd_rnaseq

  Public
  Fernando Goes and Thomas Hyde MDD RNA-seq project

  HTML

  •0•1•7•0•Updated Aug 27, 2024Aug 27, 2024

• bdportal

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

  JavaScript

  •0•0•2•0•Updated Aug 16, 2024Aug 16, 2024

• DLPFC_snRNAseq

  Public
  snRNA_seq portion of the spatialDLPFC project

  rstatsbioconductorsnrna-seq+ 1spatialdlpfc

  HTML

  •1•5•0•0•Updated Aug 16, 2024Aug 16, 2024

• zandiHyde_bipolar_rnaseq

  Public
  RNA-seq analysis for psychENCODE R01

  HTML

  •1•6•0•0•Updated Aug 15, 2024Aug 15, 2024

• deconvo_lute-paper

  Public
  Contains analysis for the lute software paper

  rneurosciencebioconductor+ 2transcriptomicsdeconvolution

  HTML

  •

  MIT License

  •0•1•0•0•Updated Aug 5, 2024Aug 5, 2024

• Human_DLPFC_Deconvolution

  Public
  Roff

  •0•3•0•0•Updated Aug 1, 2024Aug 1, 2024

• smokingMouse

  Public
  Provides access to smokingMouse project raw and processed data objects

  R

  •0•1•0•0•Updated Jul 30, 2024Jul 30, 2024

• dRFEtools

  Public
  dynamic Recursive Feature Elimination tools

  Python

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Jul 13, 2024Jul 13, 2024

• Habenula_Pilot

  Public
  habenulaPilot project code repository

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

  HTML

  •0•0•2•0•Updated Jul 11, 2024Jul 11, 2024

• template_project

  Public template
  Template project following the guidelines from https://lcolladotor.github.io/bioc_team_ds/organizing-your-work.html#.YzL43uzMKX0

  R

  •0•4•0•0•Updated Jun 28, 2024Jun 28, 2024

• HumanPilot

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

  analysishumanrstats+ 6biorxivbrain10xgenomicsspatial-transcriptomicsvisiumdlpfc

  HTML

  •29•70•0•0•Updated May 24, 2024May 24, 2024

• spatialDLPFC

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

  rstatsbioconductortranscriptomics+ 5spatial-transcriptomicsvisiumdlpfcspatialdlpfcvisium-spg

  HTML

  •3•17•1•0•Updated May 22, 2024May 22, 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 May 21, 2024May 21, 2024

• sex_differences_sz

  Public
  Sex differences in schizophrenia across the caudate nucleus, DLPFC, and hippocampus

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated May 11, 2024May 11, 2024