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    29 repositories

    • tfbpshiny

      Public
      A shiny app to explore a collection of yeast binding and perturbation data collected by the brent lab
      transcription-factorsgenomicsgenomics-data
      transcription-factorsgenomicsgenomics-data
      Python
      •
      Other
      •3•0•8•5•Updated Oct 12, 2026Oct 12, 2026

    • rossi_chipexo_peak_calling

      Public
      This stores scripts used to attempt to reproduce the data on yeastepigenome.org via chexmix, and scripts used to re-call peaks with macs3
      HTML
      •
      MIT License
      •0•0•0•0•Updated Oct 7, 2026Oct 7, 2026

    • htcf_spack_rstudio_server

      Public
      Shell
      •0•1•0•0•Updated Oct 2, 2026Oct 2, 2026

    • checseq_promoter_enrichment_slurm_pipeline

      Public
      checseq slurm pipeline based on Mahendrawada 2025
      Shell
      •0•0•0•0•Updated Sep 11, 2026Sep 11, 2026

    • CIDER

      Public
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 21, 2026Aug 21, 2026

    • tfbpmodeling

      Public
      A Python package for Transcription Factor Binding and Perturbation (TFBP) modeling that analyzes relationships between transcription factor binding and gene exp…
      genomicstranscriptiontranscriptionfactor
      genomicstranscriptiontranscriptionfactortf-bindingtranscriptionfactorstf-perturb
      Python
      •
      Other
      •5•0•2•8•Updated Jun 19, 2026Jun 19, 2026

    • METANet

      Public
      Data, scripts, references for reproducibility of METANets
      Jupyter Notebook
      •1•1•0•0•Updated Jun 9, 2026Jun 9, 2026

    • tfbpmodeling_paper_figures

      Public
      Code to create figures for the tfbpmodeling paper
      R
      •0•0•0•0•Updated Mar 27, 2026Mar 27, 2026

    • tfbpapi

      Public archive
      A collection of classes and functions which serve as an API to django.tfbindingandperturbation.com
      Python
      •
      Other
      •0•0•6•7•Updated Mar 16, 2026Mar 16, 2026

    • cryptococcus_net

      Public
      A TF network map for cryptococcus
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • fishnet

      Public
      Python
      •3•1•0•0•Updated Sep 30, 2025Sep 30, 2025

    • Dual_Threshold_Optimization

      Public
      Dual Threshold Optimization compares two ranked lists of features (e.g. genes) to determine the rank threshold for each list that minimizes the hypergeometric …
      bioinformaticstranscription-factorstranscription-factor-binding
      bioinformaticstranscription-factorstranscription-factor-bindingtranscriptional-regulatory-networkregulatory-networkgeneset-enrichment-analysistranscription-factor-perturbationregulatory-genomics
      Rust
      •
      MIT License
      •2•5•1•0•Updated Aug 19, 2025Aug 19, 2025

    • NetSurgeon

      Public
      NetSurgeon is a novel algorithm that utilizes genome-wide gene regulatory networks to identify interventions that force a cell toward a desired expression state
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • brentlab.github.io

      Public
      Brent Lab @ WashU
      HTML
      •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • NET-evaluation

      Public
      network evaluation package
      Shell
      •
      MIT License
      •1•0•0•0•Updated Sep 15, 2024Sep 15, 2024

    • callvariants

      Public
      A variant calling workflow suitable for both checking genotypes and processing data for BSA experiments
      Nextflow
      •
      MIT License
      •1•0•4•0•Updated Jun 6, 2024Jun 6, 2024

    • GOeval

      Public
      Gene Regulatory Network Evaluation Using Gene Ontology
      R
      •
      Other
      •0•1•3•0•Updated May 29, 2024May 29, 2024

    • trace_recalling

      Public
      Trace Recalling is a novel method for deconvoluting double traces that result from simultaneously sequencing two DNA templates. Trace Recalling identifies up to…
      Perl
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 4, 2024Mar 4, 2024

    • YeastCallingCardsDB

      Public
      A Django managed shiny app for storing and visualizing Yeast Calling Cards data
      Python
      •
      MIT License
      •0•0•1•0•Updated Nov 23, 2023Nov 23, 2023

    • rnaseq_databases_documentation

      Public
      Documentation for all organisms with active databases
      MIT License
      •0•0•1•0•Updated Aug 15, 2023Aug 15, 2023

    • iscan

      Public
      C
      •
      MIT License
      •0•1•0•0•Updated Jun 23, 2023Jun 23, 2023

    • Nscan

      Public
      N-SCAN is a suite of software for gene-structure prediction. N-SCAN is available for human and Drosophila (fruitfly).
      C
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Jun 23, 2023Jun 23, 2023

    • Twinscan

      Public
      Twinscan is a suite of software for gene-structure prediction. Twinscan is currently available for Mammals, Caenorhabditis (worm), Dicot plants, and Cryptococci…
      C
      •
      MIT License
      •0•2•0•0•Updated Jun 23, 2023Jun 23, 2023

    • eval

      Public
      Eval is a flexible tool for analyzing the performance of gene-structure prediction programs.
      Perl
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 7, 2023Jun 7, 2023

    • ppfinder

      Public
      PPFINDER is a Perl-based procedure for finding processed pseudogenes in genome annotations (GTF format). PPFINDER identifies pseudogenes using two different met…
      Perl
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 6, 2023Jun 6, 2023

    • NetProphet_3.0

      Public
      R
      •
      MIT License
      •1•3•0•0•Updated Nov 27, 2022Nov 27, 2022

    • TFPertRespExplainer

      Public
      Predict genes' response to perturbations and explains which genomic factors determine the response predictions.
      Jupyter Notebook
      •
      MIT License
      •1•3•0•0•Updated Jun 18, 2022Jun 18, 2022

    • NetProphet_2.0

      Public
      A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.
      transcription-factorsgene-expressiongene-regulation
      transcription-factorsgene-expressiongene-regulationtranscriptional-regulatory-network
      R
      •
      MIT License
      •4•14•0•0•Updated May 31, 2021May 31, 2021

    • TFA-evaluation

      Public
      Python
      •
      MIT License
      •1•2•0•0•Updated Dec 15, 2020Dec 15, 2020
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