HTSFilter: Filter replicated high-throughput transcriptome sequencing data

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This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

Author
Andrea Rau, Melina Gallopin, Gilles Celeux, and Florence Jaffrezic
Date of publication
None
Maintainer
Andrea Rau <andrea.rau@jouy.inra.fr>
License
Artistic-2.0
Version
1.14.1

View on Bioconductor

Man pages

HTSBasicFilter
Implement basic filters for transcriptome sequencing data.
HTSFilter
Calculate data-based filtering threshold for replicated...
HTSFilter-deprecated
Deprecated functions in package 'HTSFilter'
HTSFilter-package
Filter replicated high-throughput transcriptome sequencing...
normalizeData
Normalize transcriptome sequencing data.
sultan
RNA-seq data from humans in Sultan et al. (2008)

Files in this package

HTSFilter/DESCRIPTION
HTSFilter/NAMESPACE
HTSFilter/R
HTSFilter/R/HTSBasicFilter-methods.R
HTSFilter/R/HTSFilter-methods.R
HTSFilter/R/HTSFilter_package.R
HTSFilter/R/functions.R
HTSFilter/R/normalizeData.R
HTSFilter/build
HTSFilter/build/vignette.rds
HTSFilter/data
HTSFilter/data/sultan.RData
HTSFilter/inst
HTSFilter/inst/CITATION
HTSFilter/inst/NEWS
HTSFilter/inst/doc
HTSFilter/inst/doc/HTSFilter.R
HTSFilter/inst/doc/HTSFilter.Rnw
HTSFilter/inst/doc/HTSFilter.pdf
HTSFilter/inst/examples
HTSFilter/inst/examples/HTSBasicFilter.R
HTSFilter/inst/examples/HTSFilter-package.R
HTSFilter/man
HTSFilter/man/HTSBasicFilter.Rd
HTSFilter/man/HTSFilter-deprecated.Rd
HTSFilter/man/HTSFilter-package.Rd
HTSFilter/man/HTSFilter.Rd
HTSFilter/man/normalizeData.Rd
HTSFilter/man/sultan.Rd
HTSFilter/tests
HTSFilter/tests/testthat
HTSFilter/tests/testthat.R
HTSFilter/tests/testthat/test-xyz.R
HTSFilter/vignettes
HTSFilter/vignettes/Compile_HTSFilter.R
HTSFilter/vignettes/HTSFilter.Rnw
HTSFilter/vignettes/vignette_refs.bib