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    21 repositories

    • 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 p-value of the overlap of features. It then calculates a permutation based empirical p-value and an FDR
      bioinformaticstranscription-factorstranscription-factor-bindingtranscriptional-regulatory-networkregulatory-networkgeneset-enrichment-analysistranscription-factor-perturbationregulatory-genomics
      Rust
      •
      Other
      •1•4•0•0•Updated Dec 5, 2024Dec 5, 2024

    • yeastdnnexplorer

      Public
      A development environment to explore implementations of deep neural networks for predicting the relationship between transcription factor and target genes using binding and perturbation data
      Python
      •
      Other
      •3•1•13•9•Updated Nov 22, 2024Nov 22, 2024

    • NET-evaluation

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

    • yeastCCDBShiny

      Public
      Shiny front end to yeastCallingCardsDB
      R
      •
      Other
      •0•0•13•0•Updated Jun 21, 2024Jun 21, 2024

    • callvariants

      Public
      A variant calling workflow suitable for both checking genotypes and processing data for BSA experiments
      Nextflow
      •
      MIT License
      •0•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 two bases at each position of such a trace.
      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

    • brentlabRnaSeqTools

      Public
      R
      •
      Other
      •1•0•2•0•Updated Aug 8, 2023Aug 8, 2023

    • iscan

      Public
      C
      •
      MIT License
      •0•0•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

    • dockerize_rstudio_server

      Public
      Shell
      •0•1•0•0•Updated Jun 14, 2023Jun 14, 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 methods, and creates a GTF file with pseudogene coordinates that can be used for masking the genome sequence.
      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•2•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•2•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-regulationtranscriptional-regulatory-network
      R
      •
      MIT License
      •5•13•0•0•Updated May 31, 2021May 31, 2021

    • rnaseq_metadata_frontend

      Public
      Front end for the RNASeq metadata database(s)
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated May 17, 2021May 17, 2021

    • TFA-evaluation

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