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/HumanPilot
Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
LieberInstitute/spatialDLPFC
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
LieberInstitute/zandiHyde_bipolar_rnaseq
RNA-seq analysis for psychENCODE R01
LieberInstitute/DLPFC_snRNAseq
snRNA_seq portion of the spatialDLPFC project
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/template_project
Template project following the guidelines from https://lcolladotor.github.io/bioc_team_ds/organizing-your-work.html#.YzL43uzMKX0
LieberInstitute/DeconvoBuddies
Helper Functions for LIBD Deconvolution
LieberInstitute/Human_DLPFC_Deconvolution
LieberInstitute/Visium_SPG_AD
Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.
LieberInstitute/Kleinman_EatingDisorders_RNASeq
LieberInstitute/sex_differences_sz
Sex differences in schizophrenia across the caudate nucleus, DLPFC, and hippocampus
LieberInstitute/slurmjobs
Helper functions for working with SLURM from R
LieberInstitute/deconvo_lute-paper
Contains analysis for the lute software paper
LieberInstitute/dRFEtools
dynamic Recursive Feature Elimination tools
LieberInstitute/globus
LIBD Globus Share Endpoints
LieberInstitute/goesHyde_mdd_rnaseq
Fernando Goes and Thomas Hyde MDD RNA-seq project
LieberInstitute/ls_molecular-profiling
ls_molecular-profiling
LieberInstitute/smokingMouse
Provides access to smokingMouse project raw and processed data objects
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/Habenula_Pilot
habenulaPilot project code repository
LieberInstitute/ANCR
Scripts for "Network-wide risk convergence in gene co-expression identifies reproducible genetic hubs of schizophrenia risk"
LieberInstitute/bdportal
Brain data portal at LIBD. Not only brain data.
LieberInstitute/jhpce_module_source
JHPCE module source files
LieberInstitute/qsvaR
Quality Surrogate Variable Analysis for Degradation Correction
LieberInstitute/smoking-nicotine-mouse
Smoking mouse project
LieberInstitute/spatial_DG_lifespan
Spatial transcriptomics (Visium) in dentate gyrus of hippocampus over the lifespan
LieberInstitute/spatial_hpc
Repository for the spatial (U01) hippocampus (hipc) project
LieberInstitute/visiumStitched_brain
Example human brain data used for https://research.libd.org/visiumStitched/.