Projects in Awesome Lists by LieberInstitute

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.

hisat2 nextflow pipeline rna-seq-pipeline rnaseq rstats speaqeasy

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/zandihyde_bipolar_rnaseq

RNA-seq analysis for psychENCODE R01

Last synced: 31 Jan 2026

https://github.com/lieberinstitute/dlpfc_snrnaseq

snRNA_seq portion of the spatialDLPFC project

bioconductor rstats snrna-seq spatialdlpfc

Last synced: 01 Feb 2026

https://github.com/lieberinstitute/deconvobuddies

Helper Functions for LIBD Deconvolution

bioconductor deconvolution rstats

Last synced: 11 Dec 2025

https://github.com/lieberinstitute/rnaseq-pipeline

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

rnaseq rstats speaqeasy

Last synced: 07 May 2025

https://github.com/lieberinstitute/treg

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

bioconductor deconvolution rnascope rstats scrna-seq smfish snrna-seq treg

Last synced: 07 May 2025

https://github.com/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.

alzheimers-disease bioconductor rstats spatial-transcriptomics transcriptomics visium visium-spg visium-spg-ad

Last synced: 06 Jan 2026

https://github.com/lieberinstitute/recount.bwtool

Fast coverage matrices from recount data using bwtool

annotation-agnostic bioconductor bwtool count r recount rnaseq rstats

Last synced: 07 May 2025

https://github.com/lieberinstitute/brainrnacompartments

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

Last synced: 14 Oct 2025

https://github.com/lieberinstitute/jhpce_module_config

JHPCE module configuration files

Last synced: 07 May 2025

https://github.com/lieberinstitute/recountworkflow

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

annotation-agnostic bioconductor count derfinder deseq2 exon gene human illumina junction r recount rnaseq rstats

Last synced: 07 May 2025

https://github.com/lieberinstitute/template_project

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

Last synced: 14 Jul 2025

https://github.com/lieberinstitute/marchionni_projects

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

biorxiv fantom fantom5 fantom6 lncrna recount recount2 rstats

Last synced: 26 Jul 2025

https://github.com/lieberinstitute/human_dlpfc_deconvolution

Last synced: 07 Feb 2026

https://github.com/lieberinstitute/capture

Ca

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/bla_crossspecies

Collaboration between Costa, Martinowich, and Hicks labs investigating basolateral amygdala cell-types across huamn and non-human primate species.

Last synced: 11 Oct 2025

https://github.com/lieberinstitute/biocmap

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

nextflow wgbs

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/scmeformer

Last synced: 06 Aug 2025

https://github.com/lieberinstitute/libd_va_ptsd_rnaseq_4region

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/spatial_hpc

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

Last synced: 04 Feb 2026

https://github.com/lieberinstitute/pths_mouse

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

bioinformatics molecular-psychiatry mouse pths rna-seq-analysis

Last synced: 05 Jan 2026

https://github.com/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/.

bioconductor limma nextflow nextflow-pipelines rnaseq-pipeline rstats speaqeasy

Last synced: 09 Feb 2026

https://github.com/lieberinstitute/kleinman_eatingdisorders_rnaseq

Last synced: 27 Jan 2026

https://github.com/lieberinstitute/brain-epigenomics

dna-methylation rna-seq rstats

Last synced: 07 May 2025

https://github.com/lieberinstitute/brain_wgcna

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

Last synced: 03 Sep 2025

https://github.com/lieberinstitute/smoking_dlpfc_devel

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

differential-expression-analyses rna-seq-analysis

Last synced: 16 Jun 2025

https://github.com/lieberinstitute/recount3-docs

Documentation for all things related to `recount3`

bioconductor hg38 human mm10 mouse recount recount2 recount3 rnaseq rstats

Last synced: 14 Feb 2026

https://github.com/lieberinstitute/slurmjobs

Helper functions for working with SLURM from R

rstats slurm

Last synced: 07 May 2025

https://github.com/lieberinstitute/qsva_brain

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

brainseqphase2 degradation rnaseq rstats schizophrenia sczd

Last synced: 30 Jan 2026

https://github.com/lieberinstitute/sex_differences_sz

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

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/wgbs_meqtl_analysis

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/oxt_trap_seq

RNA-seq of Oxt neurons

Last synced: 10 Oct 2025

https://github.com/lieberinstitute/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

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/aanri_phase1

AANRI Phase 1

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/brainstorm

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

genotype quality-control rna-seq rstats

Last synced: 13 Feb 2026

https://github.com/lieberinstitute/smokingmouse

Provides access to smokingMouse project raw and processed data objects

Last synced: 16 Jun 2025

https://github.com/lieberinstitute/drfetools

dynamic Recursive Feature Elimination tools

Last synced: 01 Oct 2025

https://github.com/lieberinstitute/spatial_hyp

Last synced: 19 Feb 2026

https://github.com/lieberinstitute/expr_shape

Explore expression shapes using recount2 GTEx data

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/speaqeasy-example

Full length example for SPEAQeasy

rnaseq rstats speaqeasy

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/code_for_wgcna_ms_er

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/treg_paper

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

Last synced: 22 Jul 2025

https://github.com/lieberinstitute/dg_hippo_paper

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/cst_trap_seq

Last synced: 03 Jul 2025

https://github.com/lieberinstitute/smoking-nicotine-mouse

Smoking mouse project

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/jaffe_onboarding

Jaffe lab onboarding materials

onbording rstats website

Last synced: 19 Mar 2026

https://github.com/lieberinstitute/hallock_lfp

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

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/deconvo_review-paper

Deconvolution commentary related to R01MH123183

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/recountworkshop

Package for the recount workshop for BioC2017

annotation-agnostic bioconductor count derfinder deseq2 exon gene human illumina junction r recount rnaseq rstats

Last synced: 23 Mar 2025

https://github.com/lieberinstitute/spatialtissuelocator

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

Last synced: 07 Oct 2025

https://github.com/lieberinstitute/mirna_kit_comparison

Last synced: 20 Jul 2026

https://github.com/lieberinstitute/visiumstitched_brain

Example human brain data used for https://research.libd.org/visiumStitched/.

bioconductor rstats spatial spatiallibd transcriptomics visium visiumstitched

Last synced: 08 Feb 2026

https://github.com/lieberinstitute/ls_molecular-profiling

ls_molecular-profiling

Last synced: 14 Feb 2026

https://github.com/lieberinstitute/lff_spatial_erc

LFF_spatial_ERC

Last synced: 15 Feb 2026

https://github.com/lieberinstitute/goeshyde_mdd_rnaseq

Fernando Goes and Thomas Hyde MDD RNA-seq project

Last synced: 19 Mar 2026

https://github.com/lieberinstitute/deconvo_lute-paper

Contains analysis for the lute software paper

bioconductor deconvolution neuroscience r transcriptomics

Last synced: 16 Jul 2025

https://github.com/lieberinstitute/visiumstitched

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

10xgenomics bioconductor rstats spatial-transcriptomics spatialexperiment spatiallibd visium

Last synced: 23 Mar 2025

Last synced: 05 Jan 2026

Last synced: 04 Jan 2026

https://github.com/lieberinstitute/brainflowprobes

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

bioconductor rstats

Last synced: 13 Feb 2026

Last synced: 18 Jul 2026

Last synced: 01 Feb 2026

https://github.com/lieberinstitute/spatial_nac

Paired snRNA-seq/Visium for human NAc

Last synced: 18 Feb 2026