ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
By M. Morgan, Simon Anders, M. Lawrence, Patrick Aboyoun, Hervé Pagès, Robert Gentleman. Bioinform., 2009
409 citations recorded by the source corpus.
Summary: ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources. Availability and Implementation: This package is implemented in R and available at the Bioconductor web site; the package contains a ‘vignette’ outlining typical work flows. Contact: mtmorgan@fhcrc.org
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/aad47baacb0fed142b66c5ef21a817c14f1d54de
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In Molecular Biology
- Wolfgang Huber
- Martin T. Morgan
- Michael F. Lawrence
- Hervé Pagès
- Vincent J. Carey
- Robert Gentleman
- Gordon K. Smyth
- Jeffrey T. Leek
Citations in the corpus
- Software for Computing and Annotating Genomic Ranges (2013, positive): “We parsed the MAQ output using the ShortRead package [7], and the alignments for three chromosomes (chr10, chr11 and chr12) were extracted for use as a demonstration data set in the chipseq package [8].”
- AdapterRemoval: easy cleaning of next-generation sequencing reads (2012, neutral): “trimLRPatterns Yes Yes Yes No No No No No No [25,26]”