Repositories list

• loxodes-bleties-workflow

  Public
  genome-assemblysnakemake-workflowloxodes+ 1internal-eliminated-sequences

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated May 6, 2024May 6, 2024

• DevPF_code

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Jan 29, 2024Jan 29, 2024

• loxodes-assembly-workflow

  Public
  genome-assemblysnakemake-workflowloxodes

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 10, 2023Nov 10, 2023

• pogigwasc-utils

  Public
  scriptsgene-prediction

  Python

  •

  MIT License

  •0•0•1•0•Updated Nov 10, 2023Nov 10, 2023

• eugene

  Public
  Eugene is an integrative genome annotation software

  C++

  •1•0•0•0•Updated Oct 30, 2023Oct 30, 2023

• trf_utils

  Public
  Scripts to reformat TRF output files

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023

• loxodes-srna-workflow

  Public
  small RNA library processing and analysis

  srnasnakemake-workflowloxodes

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023

• loxodes-pogigwasc-workflow

  Public
  Pogigwasc gene prediction of Loxodes magnus genome

  genome-annotationgene-predictionsnakemake-workflow+ 1loxodes

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023

• loxodes-nucleosomes-workflow

  Public
  nucleosome-positioningsnakemake-workflowloxodes

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023

• loxodes-kmer-comp

  Public
  genomicssnakemake-workflowloxodes

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023

• loxodes-intronarrator-workflow

  Public
  Empirical intron annotation for Loxodes magnus genome assembly

  genome-annotationsnakemake-workflowintron-prediction+ 1loxodes

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023

• mnutils

  Public
  MNase-seq utilities

  nucleosome-positioning

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023

• ICOP_code

  Public
  Software for analysis of data associated with investigations of Paramecium ICOP proteins

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•1•0•Updated Aug 9, 2023Aug 9, 2023

• Intronarrator

  Public
  Gene prediction using empirically determined introns

  genepredictionintrons

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•2•1•0•Updated Oct 14, 2022Oct 14, 2022

• pogigwasc

  Public
  Prediction of genes in genomes with ambiguous stop codons

  genetic-codegene-prediction

  Java

  •

  MIT License

  •0•1•1•0•Updated Sep 28, 2022Sep 28, 2022

• IES_nuc_density

  Public
  Scripts and notebook for analysis IES nucleosome densities

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•1•0•Updated Sep 13, 2022Sep 13, 2022

• hisat2

  Public
  Graph-based alignment (Hierarchical Graph FM index)

  C++

  •

  GNU General Public License v3.0

  •119•0•0•0•Updated Aug 18, 2022Aug 18, 2022

• karyocode-analysis-busco

  Public
  genetic-codesnakemake-workflowkaryocode

  Shell

  •0•0•0•0•Updated Jul 21, 2022Jul 21, 2022

• bleties-test-tthe

  Public
  Benchmarking BleTIES with Tetrahymena long read data

  genome-editinginternal-eliminated-sequencesbleties

  Jupyter Notebook

  •0•0•0•0•Updated Jun 15, 2022Jun 15, 2022

• bleties-test-ptet

  Public
  Benchmarking BleTIES with simulated long reads

  genome-editinginternal-eliminated-sequencesbleties

  Jupyter Notebook

  •0•0•0•0•Updated Jun 15, 2022Jun 15, 2022

• karyocode-analysis-porc

  Public
  genetic-codesnakemake-workflowkaryocode

  Python

  •0•0•0•0•Updated Jun 15, 2022Jun 15, 2022

• karyocode-workflow

  Public
  genetic-codesnakemake-workflowkaryocode

  Python

  •0•0•0•0•Updated Jun 15, 2022Jun 15, 2022

• bleties

  Public
  IES retention analysis from PacBio CCS reads

  bioinformaticsgenome-assemblygenome-editing+ 1internal-eliminated-sequences

  Python

  •

  MIT License

  •2•4•13•0•Updated May 18, 2022May 18, 2022

• gbtquick

  Public
  lazy person's blobtools2

  Python

  •

  MIT License

  •1•1•0•0•Updated Apr 21, 2022Apr 21, 2022

• PORC

  Public
  Prediction Of Reassigned Codons

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 14, 2022Apr 14, 2022

• codetta

  Public
  Python

  •

  Other

  •9•0•0•0•Updated Dec 17, 2021Dec 17, 2021

• ParTIES

  Public
  PARamecium Toolbox for Interspersed DNA Elimination Studies

  Perl

  •

  GNU General Public License v3.0

  •4•0•0•0•Updated Aug 20, 2021Aug 20, 2021

• telomere-kmer-search

  Public
  Python

  •0•0•0•0•Updated Feb 23, 2021Feb 23, 2021

• Porechop

  Public
  adapter trimmer for Oxford Nanopore reads

  C++

  •

  GNU General Public License v3.0

  •128•0•0•0•Updated Aug 30, 2019Aug 30, 2019