Pinned Repositories
10xPilot_snRNAseq-human
10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC
Alzheimers_DNAm
Epigenome-wide analysis of DNA methylation from Alzheimer's patients and unaffected controls
dotdotdot
Example vignette for dotdotdot software
HumanPilot
Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
INTERACT
megadepth
R interface to megadepth: BigWig and BAM related utilities
recount3
Explore and download data from the recount3 project
spatialDLPFC
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
spatialLIBD
Code for the spatialLIBD R/Bioconductor package and shiny app
VistoSeg
Image processing pipeline for spatial projects
Lieber Institute for Brain Development 's Repositories
LieberInstitute/spatialLIBD
Code for the spatialLIBD R/Bioconductor package and shiny app
LieberInstitute/recount3
Explore and download data from the recount3 project
LieberInstitute/megadepth
R interface to megadepth: BigWig and BAM related utilities
LieberInstitute/recountWorkshop2020
BioC2020 workshop: Human RNA-seq data from recount2 and related packages
LieberInstitute/jaffelab
R package with commonly used functions by the Jaffe lab
LieberInstitute/shinycsv
Interactively explore a table
LieberInstitute/jhpce_module_config
JHPCE module configuration files
LieberInstitute/recountWorkflow
Public repo for the recount Bioconductor workflow that is visible at http://bioconductor.org/help/workflows/
LieberInstitute/TREG
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
LieberInstitute/DeconvoBuddies
Helper Functions for LIBD Deconvolution
LieberInstitute/Human_DLPFC_Deconvolution
LieberInstitute/SPEAQeasyWorkshop2020
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/.
LieberInstitute/brainstorm
Matching genotype and RNA-seq data to conform IDs of brain samples
LieberInstitute/recount3-docs
Documentation for all things related to `recount3`
LieberInstitute/slurmjobs
Helper functions for working with SLURM from R
LieberInstitute/brainflowprobes
A package to annotate and visualize expression of candidate BrainFlow probe sequences.
LieberInstitute/globus
LIBD Globus Share Endpoints
LieberInstitute/smoking-nicotine-mouse
Smoking mouse project
LieberInstitute/smokingMouse
Provides access to smokingMouse project raw and processed data objects
LieberInstitute/spatial_hpc
Repository for the spatial (U01) hippocampus (hipc) project
LieberInstitute/SPEAQeasy-example
Full length example for SPEAQeasy
LieberInstitute/visiumStitched
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/.
LieberInstitute/spatial_DG_lifespan
Spatial transcriptomics (Visium) in dentate gyrus of hippocampus over the lifespan
LieberInstitute/visiumStitched_brain
Example human brain data used for https://research.libd.org/visiumStitched/.
LieberInstitute/GenomicState
Build and access GenomicState objects for use with derfinder tools from sources like Gencode
LieberInstitute/jhpce_module_source
JHPCE module source files
LieberInstitute/qsvaR
Quality Surrogate Variable Analysis for Degradation Correction
LieberInstitute/scMeformer
LieberInstitute/sgejobs
Helper functions for SGE jobs at JHPCE
LieberInstitute/spatial_HYP