Package: appreci8R 1.25.0
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_1.25.0.tar.gz
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appreci8R_1.25.0.tgz(r-4.4-any)appreci8R_1.25.0.tgz(r-4.3-any)
appreci8R_1.25.0.tar.gz(r-4.5-noble)appreci8R_1.25.0.tar.gz(r-4.4-noble)
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appreci8R.pdf |appreci8R.html✨
appreci8R/json (API)
NEWS
| # Install 'appreci8R' in R: |
| install.packages('appreci8R', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:appreci8R-1.23.0(bioc 3.20)appreci8R-1.22.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
variantdetectiongeneticvariabilitysnpvariantannotationsequencing
Last updated 23 days agofrom:2946ad7e8f. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | NOTE | Oct 30 2024 |
Exports:annotateappreci8RshinycombineOutputdetermineCharacteristicsevaluateCovAndBQfilterTargetfinalFiltrationnormalize
Dependencies:abindade4AnnotationDbiAnnotationHubaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobBSgenomeBSgenome.Hsapiens.UCSC.hg19bslibcachemclicodetoolscommonmarkCOSMIC.67cpp11crayoncrosstalkcurlDBIdbplyrDelayedArraydigestdplyrDTevaluatefansifastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGenomicScoresglueGO.dbgraphHDF5ArrayhighrhmsHomo.sapienshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesjquerylibjsonliteKEGGRESTknitrlambda.rlaterlatticelazyevallifecycleMafDb.1Kgenomes.phase3.hs37d5MafDb.ExAC.r1.0.hs37d5MafDb.gnomADex.r2.1.hs37d5magrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslopenxlsxorg.Hs.eg.dbOrganismDbipillarpixmappkgconfigplogrpngPolyPhen.Hsapiens.dbSNP131prettyunitsprogresspromisespurrrR6rappdirsRBGLRcppRcppArmadilloRCurlrentrezrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssasssegmentedseqinrshinyshinyjsSIFT.Hsapiens.dbSNP137snowSNPlocs.Hsapiens.dbSNP144.GRCh37sourcetoolsspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexTxDb.Hsapiens.UCSC.hg19.knownGenetxdbmakerUCSC.utilsutf8VariantAnnotationvctrswithrxfunXMLxml2xtableXtraSNPlocs.Hsapiens.dbSNP144.GRCh37XVectoryamlzipzlibbioc
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 |
