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    22 repositories

    • Reindeer-use-cases

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

    • KamScan

      Public
      A simple Python script for scanning a kmer count matrix and select lines with desired statistics
      Python
      •0•2•0•0•Updated Nov 21, 2024Nov 21, 2024

    • Annotate-contigs

      Public
      Generalized contig annotation (dekupl-annot 2.0 in python)
      Python
      •0•3•1•0•Updated Nov 19, 2024Nov 19, 2024

    • 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•0•0•0•Updated Oct 23, 2024Oct 23, 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

    • mkprobe

      Public
      Build contigs from contiguous kmers stored as fasta files
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • KaMRaT

      Public
      C++
      •2•12•1•0•Updated Jun 19, 2024Jun 19, 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

    • countTags

      Public
      Count few Tags fast and in large number of fastq file
      C++
      •0•0•0•0•Updated Jun 4, 2020Jun 4, 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-seqpipelinedifferential-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