Discover LieberInstitute/Code_for_WGCNA_MS

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LieberInstitute

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spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

HumanPilot

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

HTML

recount3

Explore and download data from the recount3 project

10xPilot_snRNAseq-human

10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC

HTML

dotdotdot

Example vignette for dotdotdot software

MATLAB

spatialDLPFC

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

HTML

VistoSeg

Image processing pipeline for spatial projects

MATLAB

megadepth

R interface to megadepth: BigWig and BAM related utilities

brainseq_phase2

BrainSeq Phase II project lead by LIBD for the BrainSeq Consortium

HTML

Alzheimers_DNAm

Epigenome-wide analysis of DNA methylation from Alzheimer's patients and unaffected controls

recount-brain

Code and analyses for the recount-brain project

HTML

INTERACT

Python

recountWorkshop2020

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

BrainSeq_Phase1

code from brainseq phase 1 paper

shinycsv

Interactively explore a table

jaffelab

R package with commonly used functions by the Jaffe lab

zandiHyde_bipolar_rnaseq

RNA-seq analysis for psychENCODE R01

HTML

libd_stem_timecourse

HTML

DLPFC_snRNAseq

snRNA_seq portion of the spatialDLPFC project

HTML

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.

HTML

SUFI

An automated approach to spectral unmixing of fluorescent images

MATLAB

recount.bwtool

Fast coverage matrices from recount data using bwtool

jhpce_module_config

JHPCE module configuration files

Lua

RNAseq-pipeline

Original version of the RNA-seq pipeline implemented in SPEAQeasy at https://github.com/LieberInstitute/SPEAQeasy.

TREG

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

recountWorkflow

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

TeX

BrainRNACompartments

Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation

template_project

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

marchionni_projects

Collaboration with Luigi Marchionni (JHU) and RIKEN with recount2 data

Shell

brain-epigenomics

DeconvoBuddies

Helper Functions for LIBD Deconvolution

LIBD_VA_PTSD_RNAseq_4Region

PTHS_mouse

Scripts used to analyze RNAseq data from mouse models of Pitt-Hopkins Syndrome related to Phan, Bohlen et al.

PostScript

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.

HTML

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/.

Human_DLPFC_Deconvolution

Roff

recount3-docs

Documentation for all things related to `recount3`

qsva_brain

qSVA adapted for 2 brain regions as part of the BrainSeq Phase II project

HTML

CaPTure

MATLAB

wgbs_meqtl_analysis

sex_differences_sz

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

Jupyter Notebook

Brain_WGCNA

Scripts for the WGCNA paper: Schizophrenia risk genes converge into divergent co-expression pathways reflecting brain development across regions and age periods

oxt_trap_seq

RNA-seq of Oxt neurons

Smoking_DLPFC_Devel

Code used to generate results for the paper: Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome

brainstorm

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

aanri_phase1

AANRI Phase 1

Python

Kleinman_EatingDisorders_RNASeq

slurmjobs

Helper functions for working with SLURM from R

brainflowprobes

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

TREG_paper

Analysis for the TREG paper by L. A. Huuki-Myers et al, 2022

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/.

Hallock_LFP

Sundry functions for analyzing continuously sampled LFP/EEG data. Used in "Hallock, Wang, & Griffin, 2016, J Neurosci" paper.

MATLAB

living_brain_reanalysis

Re-analyses of the "A study of gene expression in the living human brain" pre-print DOI: https://doi.org/10.1101/2023.04.21.23288916

Roff

smokingMouse

Provides access to smokingMouse project raw and processed data objects

jaffe_onboarding

Jaffe lab onboarding materials

HTML

SpatialTissueLocator

Data and code for a shiny app to look at ST spots over histology images

cst_trap_seq

miRNA_Kit_Comparison

HTML

SPEAQeasy-example

Full length example for SPEAQeasy

Shell

expr_shape

Explore expression shapes using recount2 GTEx data

recountWorkshop

Package for the recount workshop for BioC2017

HTML

BiocMAP

Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow

HTML

dg_hippo_paper

deconvo_review-paper

Deconvolution commentary related to R01MH123183

ls_molecular-profiling

HTML

deconvo_lute-paper

Contains analysis for the lute software paper

HTML

goesHyde_mdd_rnaseq

Fernando Goes and Thomas Hyde MDD RNA-seq project

HTML

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