Repositories list

• GWAS_E2G_benchmarking

  Public
  Benchmark enhancer-gene predictions against fine-mapped GWAS variants

  R

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• eQTLEnrichment

  Public
  R

  •0•1•0•0•Updated Nov 8, 2024Nov 8, 2024

• scE2G

  Public
  Pipeline to run sc-E2G

  Python

  •

  MIT License

  •0•4•0•0•Updated Nov 1, 2024Nov 1, 2024

• variant-flowfish

  Public
  Analysis for Variant-FlowFISH experiments

  Python

  •

  GNU General Public License v3.0

  •0•3•1•0•Updated Oct 31, 2024Oct 31, 2024

• gene_network_evaluation

  Public
  Evaluation framework for computationally inferred gene networks from single-cell data.

  single-cell-genomicsenhancer-predictiongene-regulatory-network+ 1gene-co-expression-network

  Jupyter Notebook

  •

  GNU General Public License v2.0

  •7•9•16•0•Updated Oct 22, 2024Oct 22, 2024

• IGVF_E2G_jamboree_2024

  Public
  Helper scripts for IGVF E2G pillar project jamboree 2024

  R

  •1•0•0•0•Updated Sep 26, 2024Sep 26, 2024

• CRISPR_comparison

  Public
  Snakemake workflow for comparing E-G links to experimental data

  R

  •2•11•0•0•Updated Sep 24, 2024Sep 24, 2024

• ENCODE_rE2G

  Public
  Enhancer-Gene Prediction Pipeline based on logistic regression and ABC model

  Python

  •0•4•0•2•Updated Sep 9, 2024Sep 9, 2024

• cNMF_pipeline

  Public
  Jupyter Notebook

  •0•2•0•0•Updated Jul 17, 2024Jul 17, 2024

• encode_dataset_processing

  Public
  Code to get the encode datasets that will get run through ABC + Encode-rE2G

  Python

  •1•0•0•0•Updated Jun 7, 2024Jun 7, 2024

• crispri-flowfish

  Public
  Python

  •0•1•1•0•Updated Feb 6, 2024Feb 6, 2024

• V2G

  Public
  R

  •1•0•0•0•Updated Dec 11, 2023Dec 11, 2023

• IGVF-Y2AVE

  Public
  R

  •

  MIT License

  •1•0•0•0•Updated Oct 10, 2023Oct 10, 2023

• igvf_dataset_processing

  Public
  Processing IGVF data

  Python

  •0•0•0•0•Updated Sep 28, 2023Sep 28, 2023

• chrombpnet

  Public
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

  Jupyter Notebook

  •

  MIT License

  •34•0•0•0•Updated Jun 10, 2023Jun 10, 2023

• ABC-Max-pipeline

  Public
  HTML

  •0•1•0•0•Updated Jan 5, 2023Jan 5, 2023

• ABCGeneReference

  Public
  Create promoter/gene lists from GENCODE gtf files

  R

  •0•1•0•0•Updated Aug 27, 2022Aug 27, 2022

• SingleCellAnalysisTutorial

  Public
  HTML

  •0•0•0•0•Updated Jul 13, 2022Jul 13, 2022

• CRISPRDesigner

  Public
  Design and selection of gRNAs for pooled CRISPRi tiling screens

  Python

  •

  MIT License

  •0•1•0•0•Updated Jun 27, 2022Jun 27, 2022

• ABC-GWAS-Paper

  Public
  Code to reproduce analyses in Nasser, Bergman, Fulco, Guckelberger, Doughty et al Nature 2021

  PostScript

  •2•12•2•0•Updated Apr 8, 2021Apr 8, 2021

• hypr-seq

  Public
  Code for analyzing HyPR-seq data

  Python

  •1•0•0•0•Updated Feb 17, 2021Feb 17, 2021

• cookiecutter-snakemake-workflow

  Public template
  A cookiecutter template for Snakemake workflows

  Python

  •

  MIT License

  •37•1•0•0•Updated Jan 15, 2021Jan 15, 2021