Repositories list

• KamScan

  Public
  A simple Python script for scanning a kmer count matrix and select lines with desired statistics

  Python

  •0•2•0•0•Updated Aug 8, 2025Aug 8, 2025

• Annotate-contigs

  Public
  Generalized contig annotation (dekupl-annot 2.0 in python)

  Python

  •0•3•1•0•Updated Jul 4, 2025Jul 4, 2025

• KaMRaT

  Public
  C++

  •

  Other

  •2•13•1•0•Updated Jul 2, 2025Jul 2, 2025

• mkprobe

  Public
  Build contigs from contiguous kmers stored as fasta files

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

• RiboKast

  Public
  A reference-free translation predictor for ribo-seq data using k-mers

  Python

  •0•0•0•0•Updated May 28, 2025May 28, 2025

• RiboKastIndex

  Public
  Makes k-mer indexes from ribo-seq data

  R

  •0•0•0•0•Updated May 28, 2025May 28, 2025

• kmerator

  Public
  Prototype for decomposition of transcript or gene sequences and extraction of their specific k-mers

  Python

  •

  GNU General Public License v3.0

  •0•1•1•0•Updated May 6, 2025May 6, 2025

• countTags

  Public
  Count few Tags fast and in large number of fastq file

  C++

  •0•1•0•0•Updated Feb 6, 2025Feb 6, 2025

• Reindeer-use-cases

  Public
  0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

• kmerexplor

  Public
  KmerExploR provides information of a requested RNA-seq dataset Set.

  Python

  •

  GNU General Public License v3.0

  •0•0•1•0•Updated Oct 15, 2024Oct 15, 2024

• publication-ccle

  Public
  Scripts and data for the CCLE Transipedia publication

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Sep 20, 2024Sep 20, 2024

• REINDEER-count-validation

  Public
  R

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

• fos_builder

  Public
  companon tools for Transipedia website and Reindeer.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 5, 2024Jan 5, 2024

• meta-bam

  Public
  Sample reads from fastq files - align to genome - makes a "meta-bam" file.

  Shell

  •0•1•0•0•Updated Jul 20, 2023Jul 20, 2023

• dekupl-lung-cancer-inter-cohort

  Public
  Replicability of dekupl and gene-level predictions across 2 independent lung cancer cohorts

  Python

  •0•1•0•0•Updated Feb 7, 2022Feb 7, 2022

• dekupl-run

  Public
  Identify differentially expressed k-mers between RNA-Seq datasets

  R

  •

  MIT License

  •11•11•11•2•Updated Mar 1, 2021Mar 1, 2021

• dekupl-annotation

  Public
  Annotate DE contigs identified by DE-kupl.

  Perl

  •7•4•3•0•Updated Dec 18, 2020Dec 18, 2020

• dekupl-viewer

  Public
  Shiny app to interactively visualize DE-kupl Annotation output

  R

  •

  MIT License

  •0•2•2•0•Updated Jan 25, 2019Jan 25, 2019

• dekupl-TtestFilter

  Public
  Differential analysis of k-mer abundances.

  C

  •0•0•0•0•Updated Nov 8, 2018Nov 8, 2018

• dekupl

  Public
  Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.

  bioinformaticsrna-seqpipeline+ 2differential-expressionrna-seq-data

  2•15•3•0•Updated Oct 15, 2018Oct 15, 2018

• dekupl-joinCounts

  Public
  Join multiple k-mer abundance files into a single matrix.

  C

  •2•2•0•0•Updated Apr 15, 2018Apr 15, 2018

• dekupl-computeNF

  Public
  Compute Normalization Factors from k-mer counts table.

  C

  •0•0•2•0•Updated Mar 13, 2018Mar 13, 2018

• dekupl-testbench

  Public
  A set of test cases for dekupl-run, to make sure it really identifies differential k-mers

  0•0•0•0•Updated Feb 23, 2018Feb 23, 2018

• dekupl-mergeTags

  Public
  DE k-mers assembly procedure.

  C

  •2•0•0•0•Updated Jun 27, 2017Jun 27, 2017