Repositories list

• Human_DLPFC_Deconvolution

  Public
  Roff

  •0•3•0•0•Updated Jan 3, 2025Jan 3, 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•1•2•0•Updated Jan 3, 2025Jan 3, 2025

• spatialLIBD

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

  shinyrstatsbioconductor+ 6golem10xgenomicsspatial-transcriptomicsvisiumspatiallibdspatialexperiment

  R

  •19•88•20•1•Updated Dec 16, 2024Dec 16, 2024

• DeconvoBuddies

  Public
  Helper Functions for LIBD Deconvolution

  rstatsbioconductordeconvolution

  R

  •1•3•6•0•Updated Dec 16, 2024Dec 16, 2024

• 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•11•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

• spatial_DG_lifespan

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

  HTML

  •0•0•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

• recount3

  Public
  Explore and download data from the recount3 project

  countgener+ 12humanmouserstatsbioconductorrnaseqilluminaexon+ 5

  R

  •4•31•20•0•Updated Dec 10, 2024Dec 10, 2024

• recountWorkshop2020

  Public
  BioC2020 workshop: Human RNA-seq data from recount2 and related packages

  rstatsderfinderrecount+ 6genomicstatebioc2020recount-brainworkshopbioconductorrecount2

  HTML

  •3•8•0•0•Updated Dec 10, 2024Dec 10, 2024

• TREG

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

  rstatsbioconductorscrna-seq+ 5deconvolutionsnrna-seqrnascopesmfishtreg

  R

  •2•4•2•0•Updated Dec 10, 2024Dec 10, 2024

• qsvaR

  Public
  Quality Surrogate Variable Analysis for Degradation Correction

  humanrstatsbioconductor+ 3braindegradationqsva

  R

  •2•0•15•0•Updated Dec 10, 2024Dec 10, 2024

• slurmjobs

  Public
  Helper functions for working with SLURM from R

  slurmrstats

  R

  •1•2•2•0•Updated Dec 10, 2024Dec 10, 2024

• SPEAQeasyWorkshop2020

  Public
  EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http://research.libd.org/SPEAQeasy-example/.

  nextflowrstatsbioconductor+ 4limmanextflow-pipelinesrnaseq-pipelinespeaqeasy

  R

  •0•3•0•0•Updated Dec 10, 2024Dec 10, 2024

• shinycsv

  Public
  Interactively explore a table

  R

  •1•7•1•0•Updated Dec 10, 2024Dec 10, 2024

• sgejobs

  Public
  Helper functions for SGE jobs at JHPCE

  sgerstatsjhpce

  R

  •2•0•2•0•Updated Dec 10, 2024Dec 10, 2024

• brainstorm

  Public
  Matching genotype and RNA-seq data to conform IDs of brain samples

  quality-controlrna-seqrstats+ 1genotype

  R

  •1•2•5•0•Updated Dec 10, 2024Dec 10, 2024

• brainflowprobes

  Public
  A package to annotate and visualize expression of candidate BrainFlow probe sequences.

  rstatsbioconductor

  R

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

• smokingMouse

  Public
  Provides access to smokingMouse project raw and processed data objects

  R

  •0•1•0•0•Updated Dec 10, 2024Dec 10, 2024

• spatial_hpc

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

  HTML

  •0•1•1•0•Updated Dec 10, 2024Dec 10, 2024

• spatial_HYP

  Public
  HTML

  •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

• jhpce_module_source

  Public
  JHPCE module source files

  Shell

  •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• jhpce_module_config

  Public
  JHPCE module configuration files

  Lua

  •0•4•0•0•Updated Dec 6, 2024Dec 6, 2024

• globus

  Public
  LIBD Globus Share Endpoints

  HTML

  •1•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• scMeformer

  Public
  Python

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• visiumStitched_brain

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

  spatialrstatsbioconductor+ 4transcriptomicsvisiumspatiallibdvisiumstitched

  HTML

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• smoking-nicotine-mouse

  Public
  Smoking mouse project

  R

  •0•1•1•0•Updated Nov 7, 2024Nov 7, 2024