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alevinQC

alevinQC

alevinQC is an R tool to generate quality control reports that summarize the "alevin" output.

Topic

Transcriptomics; RNA-seq; Gene expression

Details

  • Operation: Visualisation; RNA-Seq analysis
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: MIT + file LICENSE
  • Cost: Free
  • Version name: 1.2.0
  • Maturity: Mature
  • Credit: -
  • Contact: Charlotte Soneson charlottesoneson at gmail.com
  • Collection: Bioconductor

Publications

Soneson C, Srivastava A "Generate QC reports summarizing the output from an alevin run. Reports can be generated as html or pdf files, or as shiny applications." bioconductor.org https://doi.org/10.18129/B9.bioc.alevinQC


Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590


Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600


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