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  1. collectf collectf Public

    CollecTF database implementation

    Python 5 3

  2. gpu_pssm gpu_pssm Public

    A GPU-based implementation of sliding window PSSM scoring.

    Python 4

  3. cgb cgb Public

    comparative genomics of transcriptional regulation in Bacteria

    Python 2 2

  4. vibrio-biofilm-formation vibrio-biofilm-formation Public

    In silico analysis of promoter architecture for biofilm formation genes involved in Vibrio cholerae

    Python 1

  5. ViPhy ViPhy Public

    Virus Phylogeny System

    Python 1

  6. control_seq_gen control_seq_gen Public

    Generates control sequences for motif analysis. Goal is to maintain the statistical parameters of the input sequences (i.e. nucleotide composition) without recapitulating the sites of interest.

    Python 1

Repositories

Showing 10 of 62 repositories
  • MD_GP_shape Public

    A project to generate models of regulated bacterial promoters using genetic programming

    Python 1 GPL-3.0 0 0 0 Updated Apr 10, 2024
  • SPA Public

    Code and data used to perform the tAI analysis in deCarvalho et al. (2023)

    Scheme 1 GPL-3.0 0 0 0 Updated Oct 31, 2023
  • cgb Public

    comparative genomics of transcriptional regulation in Bacteria

    Python 2 2 5 2 Updated Jul 6, 2023
  • tAI Public

    tRNA adaptation index

    Python 1 MIT 0 0 0 Updated Jun 17, 2023
  • PHageR Public

    Analysis of host transcriptional regulation on phage genome sequences

    Python 0 MIT 0 0 0 Updated May 30, 2023
  • Python 0 0 0 0 Updated May 29, 2023
  • SMD Public

    Systematic discovery of TF-binding motifs

    Python 0 GPL-3.0 1 0 0 Updated May 1, 2023
  • phylo_seq_gen Public

    Pulls sequences of a reference gene from a set of genomes. A MSA of these sequences can be used to construct a phylogeny.

    Python 0 0 0 0 Updated Apr 11, 2023
  • oprn_consv_calc Public

    Aims to determine the structural conservation (i.e. gene order) of an operon within a given taxonomic clade.

    Python 0 0 0 0 Updated Apr 11, 2023
  • ViPhy Public

    Virus Phylogeny System

    Python 1 0 0 0 Updated Mar 29, 2023