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ShortRead:FASTQ input and manipulation
This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
8 stars 12.08 score 1.8k scripts 49 dependentsbioc
easyRNASeq:Count summarization and normalization for RNA-Seq data
Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.
Maintained by Nicolas Delhomme. Last updated 5 months ago.
geneexpressionrnaseqgeneticspreprocessingimmunooncology
5.43 score 15 scripts 1 dependentsbioc
ncGTW:Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
The purpose of ncGTW is to help XCMS for LC-MS data alignment. Currently, ncGTW can detect the misaligned feature groups by XCMS, and the user can choose to realign these feature groups by ncGTW or not.
Maintained by Chiung-Ting Wu. Last updated 5 months ago.
softwaremassspectrometrymetabolomicsalignmentcpp
8 stars 4.90 score 3 scripts