Files in easyRNASeq

Count summarization and normalization for RNA-Seq data

R/easyRNASeq-internal-normalize.R R/ShortRead-methods.R R/easyRNASeq-AnnotParam-accessors.R R/easyRNASeq-BamParam-accessors.R R/easyRNASeq-islands.R R/file.exists-methods.R R/easyRNASeq-package.R R/easyRNASeq-internal-annotation.R R/IRanges-methods.R R/easyRNASeq-synthetic-transcripts.R R/show-methods.R R/easyRNASeq-internal-counts.R R/BiocFileCache.R R/AllGenerics.R R/easyRNASeq-normalize.R R/easyRNASeq-simpleRNASeq.R R/easyRNASeq-internal-methods.R R/easyRNASeq-RnaSeqParam-accessors.R R/basename-methods.R R/easyRNASeq-methods.R R/easyRNASeq-AnnotParam.R R/easyRNASeq-internal-AnnotParam-methods.R R/easyRNASeq-coverage-methods.R R/edgeR-methods.R R/GenomicRanges-methods.R R/DESeq-methods.R R/easyRNASeq-BamFileList.R R/genomeIntervals-methods.R R/AllClasses.R R/easyRNASeq-accessors.R R/easyRNASeq-BamParam.R R/easyRNASeq-counts.R R/parallel-methods.R R/print-methods.R R/Rsamtools-methods.R R/easyRNASeq-annotation.R R/easyRNASeq-RnaSeqParam.R vignettes/simpleRNASeq.Rmd vignettes/Chapters/08-Session-Info.Rmd vignettes/Chapters/03-SyntheticTranscripts.Rmd vignettes/Chapters/09-Acknowledgments.Rmd vignettes/Chapters/01-Introduction.Rmd vignettes/Chapters/07-cleanUp.Rmd vignettes/Chapters/12-Appendix.Rmd vignettes/Chapters/02-AnnotParam.Rmd vignettes/Chapters/10-Foonotes.Rmd vignettes/Chapters/11-Images.Rmd vignettes/Chapters/06-simpleRNASeq.Rmd vignettes/Chapters/05-RnaSeqParam.Rmd vignettes/Chapters/04-BamParam.Rmd man/show-methods.Rd man/easyRNASeq-annotation-methods.Rd man/easyRNASeq-island-methods.Rd man/IRanges-methods.Rd man/easyRNASeq-RnaSeqParam-accessors.Rd man/parallel-methods.Rd man/edgeR-methods.Rd man/easyRNASeq-easyRNASeq.Rd man/easyRNASeq-annotation-internal-methods.Rd man/easyRNASeq-global-variables.Rd man/easyRNASeq-synthetic-transcripts.Rd man/basename-methods.Rd man/easyRNASeq-internal-AnnotParam-methods.Rd man/easyRNASeq-AnnotParam-accessors.Rd man/easyRNASeq-correction-methods.Rd man/easyRNASeq-AnnotParam.Rd man/BiocFileCache-methods.Rd man/easyRNASeq-accessors.Rd man/easyRNASeq-summarization-methods.Rd man/file.exists-methods.Rd man/easyRNASeq-defunct-annotation-methods.Rd man/easyRNASeq-RnaSeqParam.Rd man/DESeq-methods.Rd man/ShortRead-methods.Rd man/easyRNASeq-AnnotParam-class.Rd man/easyRNASeq-RnaSeqParam-class.Rd man/easyRNASeq-package.Rd man/easyRNASeq-BamParam.Rd man/easyRNASeq-BamFileList.Rd man/easyRNASeq-simpleRNASeq.Rd man/genomeIntervals-methods.Rd man/GenomicRanges-methods.Rd man/print-methods.Rd man/Rsamtools-methods.Rd man/easyRNASeq-internal-methods.Rd man/easyRNASeq-coverage-methods.Rd man/easyRNASeq-datasets.Rd man/easyRNASeq-class.Rd man/easyRNASeq-BamParam-accessors.Rd man/easyRNASeq-summarization-internal-methods.Rd man/easyRNASeq-defunct.Rd man/easyRNASeq-BamParam-class.Rd tests/runTests.R inst/doc/08-Session-Info.Rmd inst/doc/03-SyntheticTranscripts.Rmd inst/doc/09-Acknowledgments.Rmd inst/doc/01-Introduction.Rmd inst/doc/07-cleanUp.Rmd inst/doc/12-Appendix.Rmd inst/doc/easyRNASeq.R inst/doc/02-AnnotParam.Rmd inst/doc/simpleRNASeq.R inst/doc/easyRNASeq.pdf inst/doc/10-Foonotes.Rmd inst/doc/simpleRNASeq.Rmd inst/doc/11-Images.Rmd inst/doc/06-simpleRNASeq.Rmd inst/doc/05-RnaSeqParam.Rmd inst/doc/04-BamParam.Rmd inst/doc/Chapters/08-Session-Info.Rmd inst/doc/Chapters/03-SyntheticTranscripts.Rmd inst/doc/Chapters/09-Acknowledgments.Rmd inst/doc/Chapters/01-Introduction.Rmd inst/doc/Chapters/07-cleanUp.Rmd inst/doc/Chapters/12-Appendix.Rmd inst/doc/Chapters/02-AnnotParam.Rmd inst/doc/Chapters/10-Foonotes.Rmd inst/doc/Chapters/11-Images.Rmd inst/doc/Chapters/06-simpleRNASeq.Rmd inst/doc/Chapters/05-RnaSeqParam.Rmd inst/doc/Chapters/04-BamParam.Rmd inst/unitTests/test_annotations.R inst/unitTests/test_ranges.R inst/unitTests/test_classes.R inst/unitTests/test_print.R inst/unitTests/test_variables.R inst/unitTests/test_extensions.R inst/unitTests/test_accessors.R inst/unitTests/test_methods.R