Package: appreci8R 1.30.0
Sarah Sandmann
appreci8R: appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.
Authors:
appreci8R_1.30.0.tar.gz
appreci8R_1.30.0.zip(r-4.7)appreci8R_1.30.0.zip(r-4.6)appreci8R_1.30.0.zip(r-4.5)
appreci8R_1.30.0.tgz(r-4.6-any)appreci8R_1.30.0.tgz(r-4.5-any)
appreci8R_1.30.0.tar.gz(r-4.7-any)appreci8R_1.30.0.tar.gz(r-4.6-any)
appreci8R_1.30.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
appreci8R/json (API)
NEWS
| # Install 'appreci8R' in R: |
| install.packages('appreci8R', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:appreci8R-1.31.0(bioc 3.24)appreci8R-1.30.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
variantdetectiongeneticvariabilitysnpvariantannotationsequencing
Last updated from:453b6181f0 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 778 | ||
| linux-devel-x86_64 | NOTE | 1012 | ||
| source / vignettes | OK | 882 | ||
| linux-release-x86_64 | NOTE | 808 | ||
| macos-release-arm64 | NOTE | 546 | ||
| macos-oldrel-arm64 | NOTE | 593 | ||
| windows-devel | NOTE | 965 | ||
| windows-release | NOTE | 1013 | ||
| windows-oldrel | NOTE | 888 | ||
| wasm-release | OK | 677 |
Exports:annotateappreci8RshinycombineOutputdetermineCharacteristicsevaluateCovAndBQfilterTargetfinalFiltrationnormalize
Dependencies:abindade4AnnotationDbiAnnotationHubaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomeBSgenome.Hsapiens.UCSC.hg19bslibcachemcigarilloclicodetoolscommonmarkCOSMIC.67cpp11crayoncrosstalkcurlDBIdbplyrDelayedArraydigestdir.expirydplyrDTevaluatefastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGenomicScoresglueGO.dbgraphh5mreadHDF5ArrayhighrHomo.sapienshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesjquerylibjsonliteKEGGRESTknitrlambda.rlaterlatticelazyevallifecycleMafDb.1Kgenomes.phase3.hs37d5MafDb.ExAC.r1.0.hs37d5MafDb.gnomADex.r2.1.hs37d5magrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslopenxlsxorg.Hs.eg.dbOrganismDbiotelpillarpixmappkgconfigpngPolyPhen.Hsapiens.dbSNP131promisespurrrR6rappdirsRBGLRcppRcppArmadilloRCurlrentrezrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssasssegmentedSeqinfoseqinrshinyshinyjsSIFT.Hsapiens.dbSNP137snowSNPlocs.Hsapiens.dbSNP144.GRCh37sourcetoolsspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexTxDb.Hsapiens.UCSC.hg19.knownGeneUCSC.utilsutf8VariantAnnotationvctrswithrxfunXMLxtableXtraSNPlocs.Hsapiens.dbSNP144.GRCh37XVectoryamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV | appreci8R-package appreci8 appreci8R Variant Filtration |
| Annotate and filter calls | annotate |
| A user interface to perform the whole appreci8-analysis | appreci8Rshiny |
| Combine output of different variant calling tools | combineOutput |
| Determine characteristics of the calls | determineCharacteristics |
| Evaluate coverage and base quality | evaluateCovAndBQ |
| Excludes all off-target calls from further analysis. | filterTarget |
| Perform final filtration according to the appreci8-algorithm | finalFiltration |
| Normalize calls | normalize |
