Pfenning Lab
Genetic and Epigenetic data processing code from the Pfenning Lab at Carnegie Mellon University
Pittsburgh, PA
Pinned Repositories
addiction_gwas_enrichment
Scripts and data generated for the addiction GWAS enrichment and subsequent analyses.
custom_ArchR_genomes_and_annotations
R objects that contain custom ArchR genome annotations
halLiftover-postprocessing
McLean_chronic_opioid_monkey_snRNA-seq
inDrops v3 of N=8 rhesus macaque with and without chronic opioid use
ml-prototypes
nhp_snrna_striatum_analysis
The code and notebook to go along with the Medium Spiny Neuron Diversity in the Primate Nucleus Accumbens publication
OCROrthologPrediction
This repository contains models and code for predicting open chromatin status of OCR orthologs.
RERconvergeVocalLearning
TACIT
OCR-Phenotype Association from Tissue-Aware Conservation Inference Toolkit
Zoonomia_flagship2_fine-mapping
Code for polyfun fine-mapping with updated mammalian and primate genome constraint measures.
Pfenning Lab's Repositories
pfenninglab/halLiftover-postprocessing
pfenninglab/TACIT
OCR-Phenotype Association from Tissue-Aware Conservation Inference Toolkit
pfenninglab/OCROrthologPrediction
This repository contains models and code for predicting open chromatin status of OCR orthologs.
pfenninglab/addiction_gwas_enrichment
Scripts and data generated for the addiction GWAS enrichment and subsequent analyses.
pfenninglab/custom_ArchR_genomes_and_annotations
R objects that contain custom ArchR genome annotations
pfenninglab/ml-prototypes
pfenninglab/nhp_snrna_striatum_analysis
The code and notebook to go along with the Medium Spiny Neuron Diversity in the Primate Nucleus Accumbens publication
pfenninglab/RERconvergeVocalLearning
pfenninglab/Zoonomia_flagship2_fine-mapping
Code for polyfun fine-mapping with updated mammalian and primate genome constraint measures.
pfenninglab/ad_variants
pfenninglab/celltype-ML
pfenninglab/dorsal_horn_snrnaseq
The code and jupyter notebooks to go along with the manuscript: Comparison of the Cellular and Molecular Atlases of the Macaque and Mouse Dorsal Horns
pfenninglab/dorsalhorn_conserved_rna_atac_xen
pfenninglab/McLean_chronic_opioid_monkey_snRNA-seq
inDrops v3 of N=8 rhesus macaque with and without chronic opioid use
pfenninglab/Zoonomia_Cell-TACIT_fine-mapping
Machine learning models of conserved regulatory elements and human genetics of neuropsychiatric traits
pfenninglab/ad_h3k27ac_3ct_release
Code release for brain cell type-specific H3K27ac profiling of AD hippocampus and dlPFC
pfenninglab/Logan_Striatum_snRNA-seq
Single cell transcriptomics analyses in the striatum of patients with OUD
pfenninglab/Parkinsons_GittisCollab
pfenninglab/StriatumComparativeGenomics
Comparative integrative analyses of single cell datasets of the mammalian striatum
pfenninglab/sysMPRA
This repository is for sysMPRA code.
pfenninglab/vocalLearning_TACIT
Applying TACIT for evolutionary traits with rat, macaque and bat CNN model