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annotate-contigs

Generalized contig annotation (dekupl-annot 2.0 in python)

counttags

Count few Tags fast and in large number of fastq file

dekupl

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

dekupl-annotation

Annotate DE contigs identified by DE-kupl.

dekupl-computenf

Compute Normalization Factors from k-mer counts table.

dekupl-joincounts

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

dekupl-lung-cancer-inter-cohort

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

dekupl-mergetags

DE k-mers assembly procedure.

dekupl-run

Identify differentially expressed k-mers between RNA-Seq datasets

dekupl-testbench

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

dekupl-ttestfilter

Differential analysis of k-mer abundances.

dekupl-viewer

Shiny app to interactively visualize DE-kupl Annotation output

fos_builder

companon tools for Transipedia website and Reindeer.

kamrat

kamscan

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

kmerator

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

kmerexplor

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

meta-bam

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

publication-ccle

Scripts and data for the CCLE Transipedia publication

reindeer-count-validation

reindeer-use-cases