Repositories list

• cnn_pipeline

  Public
  Train CNN models on DNA sequences.

  Python

  •11 fork•11 star•1111 issues•11 pull request•Updated Apr 14, 2026Apr 14, 2026

• Transcriptional-Brain-Aging-Clock

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 21, 2026Mar 21, 2026

• halLiftover-postprocessing

  Public

  pfenninglab/halLiftover-postprocessing’s past year of commit activity
  Python

  •

  MIT License

  •55 forks•2525 stars•44 issues•00 pull requests•Updated Dec 3, 2025Dec 3, 2025

• TACIT

  Public

  pfenninglab/TACIT’s past year of commit activity
  OCR-Phenotype Association from Tissue-Aware Conservation Inference Toolkit

  Shell

  •

  MIT License

  •33 forks•1818 stars•11 issue•00 pull requests•Updated Dec 3, 2025Dec 3, 2025

• ad-blood-h3k27ac

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 25, 2025Jul 25, 2025

• context_ad_mpra

  Public
  context_ad_mpra

  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 18, 2025Jul 18, 2025

• sysMPRA

  Public
  This repository is for sysMPRA code.

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 28, 2025Apr 28, 2025

• Macaque_Multiome_DLPFC

  Public

  pfenninglab/Macaque_Multiome_DLPFC’s past year of commit activity
  Methods for analyzing monkey single cell multiomics datasets in the prefrontal cortex.

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 27, 2025Apr 27, 2025

• Logan_Striatum_snRNA-seq

  Public
  Single cell transcriptomics analyses in the striatum of patients with OUD

  HTML

  •

  MIT License

  •11 fork•33 stars•00 issues•00 pull requests•Updated Apr 15, 2025Apr 15, 2025

• ad_variants

  Public

  pfenninglab/ad_variants’s past year of commit activity
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 28, 2025Mar 28, 2025

• custom_ArchR_genomes_and_annotations

  Public

  pfenninglab/custom_ArchR_genomes_and_annotations’s past year of commit activity
  R objects that contain custom ArchR genome annotations

  Shell

  •

  GNU General Public License v3.0

  •00 forks•11 star•11 issue•00 pull requests•Updated Mar 6, 2025Mar 6, 2025

• Pierce_transgen_rat_multiome

  Public

  pfenninglab/Pierce_transgen_rat_multiome’s past year of commit activity
  Pierce lab rat nucleus accumbens single cell multiome analyses in transgenerational model of substance use predisposition

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 25, 2025Feb 25, 2025

• pig_spinal_cord_snRNA-seq_KHQ1

  Public

  pfenninglab/pig_spinal_cord_snRNA-seq_KHQ1’s past year of commit activity
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 17, 2025Feb 17, 2025

• git-tutorial

  Public

  pfenninglab/git-tutorial’s past year of commit activity
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 11, 2025Feb 11, 2025

• StriatumComparativeGenomics

  Public
  Comparative integrative analyses of single cell datasets of the mammalian striatum

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 26, 2024Nov 26, 2024

• dorsalhorn_conserved_rna_atac_xen

  Public

  pfenninglab/dorsalhorn_conserved_rna_atac_xen’s past year of commit activity
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 16, 2024Sep 16, 2024

• OCROrthologPrediction

  Public
  This repository contains models and code for predicting open chromatin status of OCR orthologs.

  Shell

  •11 fork•44 stars•11 issue•00 pull requests•Updated Jul 3, 2024Jul 3, 2024

• ml-prototypes

  Public
  Jupyter Notebook

  •00 forks•11 star•55 issues•00 pull requests•Updated Mar 2, 2024Mar 2, 2024

• RERconvergeVocalLearning

  Public

  pfenninglab/RERconvergeVocalLearning’s past year of commit activity
  R

  •11 fork•11 star•00 issues•00 pull requests•Updated Feb 9, 2024Feb 9, 2024

• McLean_chronic_opioid_monkey_snRNA-seq

  Public
  inDrops v3 of N=8 rhesus macaque with and without chronic opioid use

  HTML

  •00 forks•11 star•00 issues•00 pull requests•Updated Dec 26, 2023Dec 26, 2023

• vocalLearning_TACIT

  Public
  Applying TACIT for evolutionary traits with rat, macaque and bat CNN model

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 31, 2023May 31, 2023

• Zoonomia_Cell-TACIT_fine-mapping

  Public

  pfenninglab/Zoonomia_Cell-TACIT_fine-mapping’s past year of commit activity
  Machine learning models of conserved regulatory elements and human genetics of neuropsychiatric traits

  genomicsevolutionepigenetics+ 5

  genomicsevolutionepigeneticscomparative-genomicsenhancershuman-geneticsneuropsychiatric-disorderssubstance-use-disorder

  Jupyter Notebook

  •

  GNU General Public License v2.0

  •22 forks•11 star•00 issues•00 pull requests•Updated Feb 10, 2023Feb 10, 2023

• Zoonomia_flagship2_fine-mapping

  Public
  Code for polyfun fine-mapping with updated mammalian and primate genome constraint measures.

  Shell

  •00 forks•11 star•00 issues•00 pull requests•Updated Nov 3, 2022Nov 3, 2022

• ad_h3k27ac_3ct_release

  Public
  Code release for brain cell type-specific H3K27ac profiling of AD hippocampus and dlPFC

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 31, 2022Jul 31, 2022

• nhp_snrna_striatum_analysis

  Public
  The code and notebook to go along with the Medium Spiny Neuron Diversity in the Primate Nucleus Accumbens publication

  Jupyter Notebook

  •11 fork•11 star•00 issues•00 pull requests•Updated Mar 25, 2022Mar 25, 2022

• celltype-ML

  Public

  pfenninglab/celltype-ML’s past year of commit activity
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 21, 2022Jan 21, 2022

• dorsal_horn_snrnaseq

  Public

  pfenninglab/dorsal_horn_snrnaseq’s past year of commit activity
  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

  single-cell-rna-seqdorsal-horn

  single-cell-rna-seqdorsal-horn

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2021Sep 2, 2021

• Parkinsons_GittisCollab

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 18, 2021Aug 18, 2021

• addiction_gwas_enrichment

  Public
  Scripts and data generated for the addiction GWAS enrichment and subsequent analyses.

  HTML

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jun 1, 2021Jun 1, 2021