Introduction | Creation and masking | Analytic utilities | Exporting to file | Session Information
Package: MultipleAlignment 0.99.4
Hervé Pagès
MultipleAlignment: Representation of multiple sequence alignments in Bioconductor
The package implements a set of S4 classes (DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment) for representing Multiple Sequence Alignments (MSA). The classes allow users to represent groups of aligned DNA, RNA or amino acid sequences as a single object. The package also provides functions to read/write such object from/to traditional MSA file formats including Stockholm and Clustal.
Authors:
MultipleAlignment_0.99.4.tar.gz
MultipleAlignment_0.99.4.zip(r-4.7)MultipleAlignment_0.99.4.zip(r-4.6)MultipleAlignment_0.99.4.zip(r-4.5)
MultipleAlignment_0.99.4.tgz(r-4.6-any)MultipleAlignment_0.99.4.tgz(r-4.5-any)
MultipleAlignment_0.99.4.tar.gz(r-4.7-any)MultipleAlignment_0.99.4.tar.gz(r-4.6-any)
MultipleAlignment_0.99.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MultipleAlignment/json (API)
| # Install 'MultipleAlignment' in R: |
| install.packages('MultipleAlignment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/multiplealignment/issues
On BioConductor:MultipleAlignment-0.99.3(bioc 3.24)
alignmentmultiplesequencealignmentgeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package
Last updated from:a3f8b65658. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 163 | ||
| linux-devel-x86_64 | OK | 156 | ||
| source / vignettes | OK | 178 | ||
| linux-release-x86_64 | OK | 217 | ||
| macos-release-arm64 | OK | 154 | ||
| macos-oldrel-arm64 | OK | 103 | ||
| windows-devel | OK | 125 | ||
| windows-release | OK | 108 | ||
| windows-oldrel | OK | 103 | ||
| wasm-release | OK | 105 |
Exports:AAMultipleAlignmentalphabetFrequencyas.matrixcoercecolmaskcolmask<-consensusMatrixconsensusStringconsensusViewsdetailDNAMultipleAlignmentmaskeddimmaskedncolmaskednrowmaskedratiomaskGapsmaskMotifncharncolnrowreadAAMultipleAlignmentreadDNAMultipleAlignmentreadRNAMultipleAlignmentRNAMultipleAlignmentrowmaskrowmask<-rownamesseqtypeshowunmaskedupdateObjectwrite.phylip
Dependencies:BiocGenericsBiostringscrayongenericsIRangesS4VectorsSeqinfoXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Show (display) detailed object content | detail |
| MultipleAlignment objects | AAMultipleAlignment AAMultipleAlignment-class as.character,MultipleAlignment-method as.matrix,MultipleAlignment-method class:AAMultipleAlignment class:DNAMultipleAlignment class:MultipleAlignment class:RNAMultipleAlignment coerce,character,AAMultipleAlignment-method coerce,character,DNAMultipleAlignment-method coerce,character,RNAMultipleAlignment-method coerce,MultipleAlignment,AAStringSet-method coerce,MultipleAlignment,BStringSet-method coerce,MultipleAlignment,DNAStringSet-method coerce,MultipleAlignment,RNAStringSet-method colmask colmask,MultipleAlignment-method colmask<- colmask<-,MultipleAlignment,ANY-method colmask<-,MultipleAlignment,NULL-method detail,MultipleAlignment-method dim,MultipleAlignment-method DNAMultipleAlignment DNAMultipleAlignment-class maskeddim maskeddim,MultipleAlignment-method maskedncol maskedncol,MultipleAlignment-method maskednrow maskednrow,MultipleAlignment-method maskedratio,MultipleAlignment-method maskGaps maskGaps,MultipleAlignment-method maskMotif,MultipleAlignment,ANY-method MultipleAlignment MultipleAlignment-class nchar,MultipleAlignment-method ncol,MultipleAlignment-method nrow,MultipleAlignment-method RNAMultipleAlignment RNAMultipleAlignment-class rowmask rowmask,MultipleAlignment-method rowmask<- rowmask<-,MultipleAlignment,ANY-method rowmask<-,MultipleAlignment,NULL-method rownames,MultipleAlignment-method rownames<-,MultipleAlignment-method seqtype,MultipleAlignment-method show,MultipleAlignment-method unmasked,MultipleAlignment-method updateObject,AAMultipleAlignment-method updateObject,DNAMultipleAlignment-method updateObject,RNAMultipleAlignment-method |
| Read/write MultipleAlignment objects | MultipleAlignment-IO MultipleAlignment_IO readAAMultipleAlignment readDNAMultipleAlignment readRNAMultipleAlignment write.phylip |
| MultipleAlignment utilities | alphabetFrequency,MultipleAlignment-method consensusMatrix,MultipleAlignment-method consensusString,AAMultipleAlignment-method consensusString,DNAMultipleAlignment-method consensusString,MultipleAlignment-method consensusString,RNAMultipleAlignment-method consensusViews consensusViews,AAMultipleAlignment-method consensusViews,DNAMultipleAlignment-method consensusViews,MultipleAlignment-method consensusViews,RNAMultipleAlignment-method MultipleAlignment-utils MultipleAlignment_utils |
