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/spatialDLPFC
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
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/DLPFC_snRNAseq
snRNA_seq portion of the spatialDLPFC project
LieberInstitute/SPEAQeasy
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.
LieberInstitute/DeconvoBuddies
Helper Functions for LIBD Deconvolution
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/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/BLA_crossSpecies
Collaboration between Costa, Martinowich, and Hicks labs investigating basolateral amygdala cell-types across huamn and non-human primate species.
LieberInstitute/Human_DLPFC_Deconvolution
LieberInstitute/spatial_hpc
Repository for the spatial (U01) hippocampus (hipc) project
LieberInstitute/recount3-docs
Documentation for all things related to `recount3`
LieberInstitute/slurmjobs
Helper functions for working with SLURM from R
LieberInstitute/globus
LIBD Globus Share Endpoints
LieberInstitute/goesHyde_mdd_rnaseq
Fernando Goes and Thomas Hyde MDD RNA-seq project
LieberInstitute/smoking-nicotine-mouse
Smoking mouse project
LieberInstitute/SPEAQeasy-example
Full length example for SPEAQeasy
LieberInstitute/Habenula_Pilot
habenulaPilot project code repository
LieberInstitute/spatial_DG_lifespan
Spatial transcriptomics (Visium) in dentate gyrus of hippocampus over the lifespan
LieberInstitute/spatial_HYP
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/Posit_Connect_shiny_apps
Code for Posit Connect R shiny apps (spatialLIBD, iSEE, ...)
LieberInstitute/qsvaR
Quality Surrogate Variable Analysis for Degradation Correction
LieberInstitute/spatialDLPFC_Visium_Sp09_pseudobulk-
Testing GitHub and Posit Connect integration using spatialDLPFC files