Package: easyRNASeq 2.43.0
Nicolas Delhomme
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.
Authors:
easyRNASeq_2.43.0.tar.gz
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easyRNASeq.pdf |easyRNASeq.html✨
easyRNASeq/json (API)
NEWS
| # Install 'easyRNASeq' in R: |
| install.packages('easyRNASeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- RobinsonDelhomme2014 - Dataset included in the package
On BioConductor:easyRNASeq-2.43.0(bioc 3.21)easyRNASeq-2.42.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressionrnaseqgeneticspreprocessingimmunooncology
Last updated 2 months agofrom:d32c68e31e. Checks:OK: 1 WARNING: 2 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | WARNING | Dec 19 2024 |
| R-4.5-linux | WARNING | Dec 19 2024 |
| R-4.4-win | NOTE | Dec 19 2024 |
| R-4.4-mac | NOTE | Dec 19 2024 |
| R-4.3-win | NOTE | Dec 19 2024 |
| R-4.3-mac | NOTE | Dec 19 2024 |
Exports:alignDataannotParamAnnotParamassayassaysBamFileListbamParamBamParambarcodePlotbasenamechastityFilterchromosomeFilterchrSizechrSize<-colDatacolnamescomposecountBycreateSyntheticTranscriptsdatasourcedemultiplexeasyRNASeqestimateDispersionsestimateSizeFactorsexonCountsfeatureCountsfetchCoveragefetchDatafileNamefileName<-geneCountsgeneModelgeneModel<-genomicAnnotationgenomicAnnotation<-getAnnotationgetBamFileListGRangesIRangeslibrarySizelibrarySize<-metadatanaPositionFilternFilterorganismNameorganismName<-pairedparallelizeplotNormalizationFactorsprecisionrangesreadAlignedreadCountsreadCounts<-readCoveragereadCoverage<-readLengthreadLength<-reduceRnaSeqParamrowRangesRPKMseqinfoseqlengthsseqlevelsseqlevels<-seqnamesseqnames<-simpleRNASeqsplitsrFilterSRFilterResultstrandstrand<-strandedstrandProtocolSummarizedExperimenttranscriptCountstutorialDatatypeunsafeAppendvalidatevignetteDatawidthwriteFastqwriteGff3yieldSize
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydeldirdigestdplyredgeRfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDatagenomeIntervalsGenomicAlignmentsGenomicRangesgluehmshttrhttr2hwriterinterpintervalsIRangesjpegjsonliteKEGGRESTlambda.rlatticelatticeExtralifecyclelimmalocfitLSDmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrpwalignR6rappdirsRColorBrewerRcppRcppEigenRhtslibrlangRsamtoolsRSQLiteS4ArraysS4VectorsShortReadsnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrxml2XVectorzlibbioc
A walkthrough the easyRNASeq package functionalities
Rendered fromsimpleRNASeq.Rmdusingknitr::rmarkdownon Dec 19 2024.Last update: 2019-11-19
Started: 2015-12-23
R / Bioconductor for High Throughput Sequence Analysis
Rendered fromeasyRNASeq.Rnwusingutils::Sweaveon Dec 19 2024.Last update: 2019-11-19
Started: 2012-02-14
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class "AnnotParam" | AnnotParam class AnnotParam-class AnnotParamCharacter-class AnnotParamObject-class |
| Class "BamParam" | BamParam class BamParam-class |
| Extend the basename function to display Rsamtools BamFile class basename | basename basename methods basename,BamFile-method basename,BamFileList-method |
| Manages the data necessary for the examples using BiocFileCache | .get_cache .get_cache,ANY-method BiocFileCache methods fetchData fetchData,character-method tutorialData tutorialData,ANY-method vignetteData vignetteData,ANY-method |
| Methods to create synthetic transcripts | createSyntheticTranscripts createSyntheticTranscripts,AnnotParamCharacter-method createSyntheticTranscripts,character-method |
| The following function are defunct: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms' | Defunct functions easyRNASeq easyRNASeq,RNAseq-method fetchAnnotation fetchCoverage fetchCoverage,RNAseq-method knownOrganisms organismName organismName,RNAseq-method organismName<- organismName<-,RNAseq-method |
| Accessors for RNAseq class | accessors chrSize chrSize,RNAseq-method chrSize<- chrSize<-,RNAseq,integer-method chrSize<-,RNAseq,list-method easyRNASeq accessors fileName fileName,RNAseq-method fileName<- fileName<-,RNAseq-method geneModel geneModel,RNAseq-method geneModel<- geneModel<-,RNAseq-method genomicAnnotation genomicAnnotation,RNAseq-method genomicAnnotation<- genomicAnnotation<-,RNAseq-method librarySize librarySize,RNAseq-method librarySize<- librarySize<-,RNAseq-method readCounts readCounts,RNAseq-method readCounts<- readCounts<-,RNAseq-method readCoverage readCoverage,RNAseq-method readCoverage<- readCoverage<-,RNAseq-method readIslands readIslands,RNAseq-method readIslands<- readIslands<-,RNAseq-method readLength readLength,RNAseq-method readLength<- readLength<-,RNAseq-method seqnames,RNAseq-method |
| Get genic annotation from a gff3/gtf file or using biomaRt | easyRNASeq annotation methods getAnnotation getAnnotation,AnnotParam-method |
| Accessors for AnnotParam class | AnnotParam-accessors datasource datasource,AnnotParam-method easyRNASeq AnnotParam accessors type,AnnotParam-method |
| AnnotParam constructor | AnnotParam AnnotParam,character-method AnnotParam,GRanges-method AnnotParam,missing-method easyRNASeq AnnotParam constructor |
| Accessors for BamParam class | BamParam-accessors easyRNASeq BamParam accessors paired paired,BamParam-method stranded stranded,BamParam-method strandProtocol strandProtocol,BamParam-method yieldSize yieldSize,BamParam-method |
| BamParam constructor | BamParam BamParam,ANY-method easyRNASeq BamParam constructor |
| easyRNASeq count table correction to RPKM | easyRNASeq correction methods RPKM RPKM,matrix,ANY,vector,vector-method RPKM,RNAseq,ANY,ANY,ANY-method RPKM,RNAseq-method |
| Compute the coverage from a Short Read Alignment file | easyRNASeq coverage methods fetchCoverage-deprecated |
| Defunct annotation function | easyRNASeq defunct annotation methods fetchAnnotation-defunct knownOrganisms-defunct |
| Extension of the GenomicRanges package | colnames colnames,GRanges-method colnames,GRangesList-method easyRNASeq GenomicRanges package extension unsafeAppend unsafeAppend,GAlignments,GAlignments-method |
| Identify expressed regions de-novo | easyRNASeq island methods findIslands findIslands,RNAseq-method |
| Accessors for RnaSeqParam class | annotParam annotParam,RnaSeqParam-method bamParam bamParam,RnaSeqParam-method countBy countBy,RnaSeqParam-method datasource,RnaSeqParam-method easyRNASeq RnaSeqParam accessors paired,RnaSeqParam-method precision precision,RnaSeqParam-method RnaSeqParam-accessors stranded,RnaSeqParam-method strandProtocol,RnaSeqParam-method yieldSize,RnaSeqParam-method |
| RnaSeqParam constructor | easyRNASeq RnaSeqParam constructor RnaSeqParam RnaSeqParam,ANY-method |
| Count methods for RNAseq object | easyRNASeq summarization methods exonCounts exonCounts,RNAseq-method featureCounts featureCounts,RNAseq-method geneCounts geneCounts,RNAseq-method islandCounts islandCounts,RNAseq-method transcriptCounts transcriptCounts,RNAseq-method |
| Dataset included in the package | easyRNASeq-datasets RobinsonDelhomme2014 |
| easyRNASeq method | easyRNASeq,character-method easyRNASeq-defunct |
| Extension for the edgeR package | edgeR additional methods plotNormalizationFactors plotNormalizationFactors,DGEList,character,character-method |
| Extend the file.exists function to check the path slot of a Rsamtools BamFile class for existence | file.exists file.exists methods file.exists,BamFile-method |
| Extension for the genomeIntervals package | genomeIntervals additional methods type,Genome_intervals-method |
| Get a BamFileList from a list of filenames | getBamFileList getBamFileList,character,character-method getBamFileList,character,missing-method |
| Extension of the IRanges package | IRanges additional methods ranges ranges,RNAseq-method |
| parallel additional methods | parallel additional methods parallelize parallelize,BamFileList,function-method parallelize,GRangesList,function-method parallelize,list,function-method parallelize,vector,function-method |
| Pretty print the content of classes from the easyRNASeq package. | print print methods print,AnnotParam-method print,BamParam-method print,RNAseq-method print,RnaSeqParam-method |
| Class "RNAseq" | RNAseq RNAseq class RNAseq-class |
| Class "RnaSeqParam" | RnaSeqParam class RnaSeqParam-class |
| Methods extending the ShortRead package functionalities | alignData barcodePlot barcodePlot,AlignedRead-method barcodePlot,DNAStringSet-method barcodePlot,ShortReadQ-method chastityFilter chastityFilter,SRFilter-method demultiplex demultiplex,AlignedRead-method demultiplex,DNAStringSet-method demultiplex,ShortReadQ-method naPositionFilter naPositionFilter,SRFilter-method ShortRead additional methods |
| Display the content of classes from the easyRNASeq package. | show methods show,AnnotParam-method show,BamParam-method show,RNAseq-method show,RnaSeqParam-method |
| simpleRNASeq method | simpleRNASeq simpleRNASeq,BamFileList,RnaSeqParam-method |
| Extension of the Rsamtools package | validate validate,BamFile-method validate,BamFileList-method |
