featureCounts is a tool to quantify RNA-seq and gDNA-seq data as counts. It is also suitable for single-cell RNA-seq (scRNA-seq) data. It supports multi-threading. The featureCounts is part of the Subread package (see links). An R version is also available as Rsubread .
Transcriptomics; Gene expression; RNA-seq
Liao Y, Smyth GK, Shi W "featureCounts: an efficient general purpose program for assigning sequence reads to genomic features." Bioinformatics. 2014 Apr 1;30(7):923-30. 2013 Nov 13. https://doi.org/10.1093/bioinformatics/btt656
PMID: 24227677
Liao Y, Smyth GK, Shi W "The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote." Nucleic Acids Res. 2013 May 1;41(10):e108. 4. https://doi.org/10.1093/nar/gkt214
PMID: 23558742
PMCID: PMC3664803
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