Introduction | Implementation | Applying VarCon to an SNV | Session info
Package: VarCon 1.21.0
Johannes Ptok
VarCon: VarCon: an R package for retrieving neighboring nucleotides of an SNV
VarCon is an R package which converts the positional information from the annotation of an single nucleotide variation (SNV) (either referring to the coding sequence or the reference genomic sequence). It retrieves the genomic reference sequence around the position of the single nucleotide variation. To asses, whether the SNV could potentially influence binding of splicing regulatory proteins VarCon calcualtes the HEXplorer score as an estimation. Besides, VarCon additionally reports splice site strengths of splice sites within the retrieved genomic sequence and any changes due to the SNV.
Authors:
VarCon_1.21.0.tar.gz
VarCon_1.21.0.zip(r-4.7)VarCon_1.21.0.zip(r-4.6)VarCon_1.21.0.zip(r-4.5)
VarCon_1.21.0.tgz(r-4.6-any)VarCon_1.21.0.tgz(r-4.5-any)
VarCon_1.21.0.tar.gz(r-4.7-any)VarCon_1.21.0.tar.gz(r-4.6-any)
VarCon_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
VarCon/json (API)
| # Install 'VarCon' in R: |
| install.packages('VarCon', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- gene2transcript - Small data frame specifying a transcript to certain genes for synonymous use.
- hbg - Donor sequences and their HBS
- hex - Hexamers and Z scores
- referenceDnaStringSet - Small DNAStringset as exemplary reference genome sequence
- transCoord - Small table as exemplary transcript table with exon coordinates
On BioConductor:VarCon-1.21.0(bioc 3.24)VarCon-1.20.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
functionalgenomicsalternativesplicing
Last updated from:b86f75b3dc. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 243 | ||
| linux-devel-x86_64 | NOTE | 528 | ||
| source / vignettes | OK | 317 | ||
| linux-release-x86_64 | NOTE | 401 | ||
| macos-release-arm64 | NOTE | 185 | ||
| macos-oldrel-arm64 | NOTE | 245 | ||
| windows-devel | NOTE | 365 | ||
| windows-release | NOTE | 351 | ||
| windows-oldrel | NOTE | 329 | ||
| wasm-release | OK | 190 |
Exports:calculateHZEIperNTcalculateMaxEntScanScoregenerateHEXplorerPlotgetMaxEntInfogetSeqInfoFromVariationprepareReferenceFastastartVarConApp
Dependencies:abindaskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomebslibcachemcigarilloclicodetoolscommonmarkcpp11crayoncurlDelayedArraydigestfarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehtmltoolshttpuvhttrIRangesisobandjquerylibjsonlitelabelinglambda.rlaterlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpillarpkgconfigpromisesR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshinyshinycssloadersshinyFilessnowsourcetoolsSparseArraySummarizedExperimentsystibbleutf8vctrsviridisLitewithrXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Generates table with HZEI scores per nucleotide of a sequence. | calculateHZEIperNT |
| Calculate MaxEntScan score of a splice site sequence | calculateMaxEntScanScore |
| Small data frame specifying a transcript to certain genes for synonymous use. | gene2transcript |
| Generates plot with HZEI values and splice site strengths from a list holding information about an SNV. | generateHEXplorerPlot |
| Generates table with MaxEntScan scores per potential SA position. | getMaxEntInfo |
| Collects information about genomic context of sequence variants. | getSeqInfoFromVariation |
| Donor sequences and their HBS | hbg |
| Hexamers and Z scores | hex |
| Imports Fasta file from filepath. | prepareReferenceFasta |
| Small DNAStringset as exemplary reference genome sequence | referenceDnaStringSet |
| Start GUI of VarCon. | startVarConApp |
| Small table as exemplary transcript table with exon coordinates | transCoord |
