Pinned Repositories
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-joinCounts
Join multiple k-mer abundance files into a single matrix.
dekupl-run
Identify differentially expressed k-mers between RNA-Seq datasets
dekupl-viewer
Shiny app to interactively visualize DE-kupl Annotation output
KaMRaT
KamScan
A simple Python script for scanning a kmer count matrix and select lines with desired statistics
meta-bam
Sample reads from fastq files - align to genome - makes a "meta-bam" file.
ANR Transipedia's Repositories
Transipedia/dekupl
Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
Transipedia/KaMRaT
Transipedia/dekupl-run
Identify differentially expressed k-mers between RNA-Seq datasets
Transipedia/dekupl-annotation
Annotate DE contigs identified by DE-kupl.
Transipedia/Annotate-contigs
Generalized contig annotation (dekupl-annot 2.0 in python)
Transipedia/dekupl-joinCounts
Join multiple k-mer abundance files into a single matrix.
Transipedia/dekupl-viewer
Shiny app to interactively visualize DE-kupl Annotation output
Transipedia/KamScan
A simple Python script for scanning a kmer count matrix and select lines with desired statistics
Transipedia/countTags
Count few Tags fast and in large number of fastq file
Transipedia/dekupl-lung-cancer-inter-cohort
Replicability of dekupl and gene-level predictions across 2 independent lung cancer cohorts
Transipedia/meta-bam
Sample reads from fastq files - align to genome - makes a "meta-bam" file.
Transipedia/publication-ccle
Scripts and data for the CCLE Transipedia publication
Transipedia/kmerator
Prototype for decomposition of transcript or gene sequences and extraction of their specific k-mers
Transipedia/REINDEER-count-validation
Transipedia/dekupl-computeNF
Compute Normalization Factors from k-mer counts table.
Transipedia/dekupl-mergeTags
DE k-mers assembly procedure.
Transipedia/dekupl-testbench
A set of test cases for dekupl-run, to make sure it really identifies differential k-mers
Transipedia/dekupl-TtestFilter
Differential analysis of k-mer abundances.
Transipedia/fos_builder
companon tools for Transipedia website and Reindeer.
Transipedia/kmerexplor
KmerExploR provides information of a requested RNA-seq dataset Set.
Transipedia/mkprobe
Build contigs from contiguous kmers stored as fasta files
Transipedia/Reindeer-use-cases