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Lieber Institute for Brain Development (LieberInstitute)

Lieber Institute for Brain Development

LieberInstitute

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Location:Baltimore, MD

Home Page:www.libd.org

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Lieber Institute for Brain Development 's repositories

spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

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HumanPilot

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

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recount3

Explore and download data from the recount3 project

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spatialDLPFC

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

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megadepth

R interface to megadepth: BigWig and BAM related utilities

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jaffelab

R package with commonly used functions by the Jaffe lab

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jhpce_module_config

JHPCE module configuration files

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recountWorkflow

Public repo for the recount Bioconductor workflow that is visible at http://bioconductor.org/help/workflows/

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TREG

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

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DeconvoBuddies

Helper Functions for LIBD Deconvolution

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Human_DLPFC_Deconvolution

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template_project

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

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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.

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sex_differences_sz

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

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slurmjobs

Helper functions for working with SLURM from R

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aanri_phase1

AANRI Phase 1

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brainflowprobes

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

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deconvo_lute-paper

Contains analysis for the lute software paper

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globus

LIBD Globus Share Endpoints

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goesHyde_mdd_rnaseq

Fernando Goes and Thomas Hyde MDD RNA-seq project

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ls_molecular-profiling

ls_molecular-profiling

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Habenula_Pilot

habenulaPilot project code repository

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Cell-type-INTERACT

Deep learning predicts DNA methylation regulatory variants in specific brain cell types and enhances fine mapping for brain disorders

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jhpce_module_source

JHPCE module source files

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qsvaR

Quality Surrogate Variable Analysis for Degradation Correction

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scMeformer

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smoking-nicotine-mouse

Smoking mouse project

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spatial_DG_lifespan

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

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spatial_hpc

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

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visiumStitched

R package containing functions useful for stitching Visium capture areas. Related to https://github.com/LieberInstitute/LS_visiumStitched

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