Repositories list

• halLiftover-postprocessing

  Public
  Python

  •4•18•3•0•Updated Dec 14, 2024Dec 14, 2024

• StriatumComparativeGenomics

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

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• custom_ArchR_genomes_and_annotations

  Public
  R objects that contain custom ArchR genome annotations

  Shell

  •

  GNU General Public License v3.0

  •0•1•1•0•Updated Sep 24, 2024Sep 24, 2024

• TACIT

  Public
  OCR-Phenotype Association from Tissue-Aware Conservation Inference Toolkit

  Shell

  •2•16•0•0•Updated Sep 19, 2024Sep 19, 2024

• dorsalhorn_conserved_rna_atac_xen

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

• OCROrthologPrediction

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

  Shell

  •0•3•1•0•Updated Jul 3, 2024Jul 3, 2024

• sysMPRA

  Public
  This repository is for sysMPRA code.

  Python

  •0•0•0•0•Updated Mar 22, 2024Mar 22, 2024

• ml-prototypes

  Public
  Jupyter Notebook

  •0•1•5•0•Updated Mar 2, 2024Mar 2, 2024

• ad_variants

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 2, 2024Mar 2, 2024

• RERconvergeVocalLearning

  Public
  R

  •0•1•0•0•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

  •0•0•0•0•Updated Dec 26, 2023Dec 26, 2023

• Logan_Striatum_snRNA-seq

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

  HTML

  •

  MIT License

  •1•0•0•0•Updated Dec 26, 2023Dec 26, 2023

• vocalLearning_TACIT

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

  Shell

  •0•0•0•0•Updated May 31, 2023May 31, 2023

• Zoonomia_Cell-TACIT_fine-mapping

  Public
  Machine learning models of conserved regulatory elements and human genetics of neuropsychiatric traits

  genomicsevolutionepigenetics+ 5comparative-genomicsenhancershuman-geneticsneuropsychiatric-disorderssubstance-use-disorder

  Jupyter Notebook

  •

  GNU General Public License v2.0

  •2•0•0•0•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

  •0•1•0•0•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

  •0•0•0•0•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

  •1•1•0•0•Updated Mar 25, 2022Mar 25, 2022

• celltype-ML

  Public
  Python

  •0•0•0•0•Updated Jan 21, 2022Jan 21, 2022

• dorsal_horn_snrnaseq

  Public
  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

  Jupyter Notebook

  •0•0•0•0•Updated Sep 2, 2021Sep 2, 2021

• Parkinsons_GittisCollab

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Aug 18, 2021Aug 18, 2021

• addiction_gwas_enrichment

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

  HTML

  •1•2•0•0•Updated Jun 1, 2021Jun 1, 2021