Package: transmogR 1.3.0
Stevie Pederson
transmogR: Modify a set of reference sequences using a set of variants
transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.
Authors:
transmogR_1.3.0.tar.gz
transmogR_1.3.0.zip(r-4.5)transmogR_1.3.0.zip(r-4.4)transmogR_1.3.0.zip(r-4.3)
transmogR_1.3.0.tgz(r-4.4-any)transmogR_1.3.0.tgz(r-4.3-any)
transmogR_1.3.0.tar.gz(r-4.5-noble)transmogR_1.3.0.tar.gz(r-4.4-noble)
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transmogR.pdf |transmogR.html✨
transmogR/json (API)
NEWS
| # Install 'transmogR' in R: |
| install.packages('transmogR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/smped/transmogr/issues
On BioConductor:transmogR-1.3.0(bioc 3.21)transmogR-1.2.0(bioc 3.20)
alignmentgenomicvariationsequencingtranscriptomevariant
Last updated 2 months agofrom:9369e9fc9b. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | OK | Dec 19 2024 |
| R-4.5-linux | OK | Dec 19 2024 |
| R-4.4-win | OK | Dec 19 2024 |
| R-4.4-mac | OK | Dec 19 2024 |
| R-4.3-win | OK | Dec 19 2024 |
| R-4.3-mac | OK | Dec 19 2024 |
Exports:digestSalmongenomogrifyindelcatoroverlapsByVarowlparYsjFromExonstransmogrifyupsetVarByColvarTypes
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArraydplyrfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehmshttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogressR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbletidyselecttzdbUCSC.utilsutf8VariantAnnotationvctrsviridisLitevroomwithrXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Parse the output from salmon | digestSalmon |
| Mogrify a genome using a set of variants | genomogrify genomogrify,BSgenome,GRanges-method genomogrify,BSgenome,VcfFile-method genomogrify,XStringSet,GRanges-method genomogrify,XStringSet,VcfFile-method genomogrify-methods |
| Substitute InDels into one or more sequences | indelcator indelcator,BSgenome,GRanges-method indelcator,DNAStringSet,GRanges-method indelcator,XString,GRanges-method |
| Count overlaps by variant type | overlapsByVar overlapsByVar,GRanges,GRanges-method overlapsByVar,GRangesList,GRanges-method overlapsByVar-methods |
| OverWrite Letters in an XStringSet | owl owl,BSgenome,GRanges-method owl,XStringSet,GRanges-method |
| Get the PAR-Y Regions From a Seqinfo Object | parY parY,character-method parY,Seqinfo-method parY-methods |
| Obtain Splice-Junctions from Exons and Transcripts | sjFromExons |
| Mogrify a transcriptome using a set of variants | transmogrify transmogrify,BSgenome,GRanges,GRanges-method transmogrify,BSgenome,VcfFile,GRanges-method transmogrify,XStringSet,GRanges,GRanges-method transmogrify,XStringSet,VcfFile,GRanges-method transmogrify-methods |
| Show Variants by Impacted Columns | upsetVarByCol |
| Identify SNVs, Insertions and Deletions | varTypes |
