Package: appreci8R 1.23.0

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:Sarah Sandmann

appreci8R_1.23.0.tar.gz
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appreci8R_1.23.0.tgz(r-4.4-any)appreci8R_1.23.0.tgz(r-4.3-any)
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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.

bioconductor-package

8 exports 0.91 score 156 dependencies

Last updated 2 months agofrom:d9c0f80852

Exports:annotate appreci8Rshiny combineOutput determineCharacteristics evaluateCovAndBQ filterTarget finalFiltration normalize

Dependencies:abind ade4 AnnotationDbi AnnotationHub askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg19 bslib cachem cli codetools commonmark COSMIC.67 cpp11 crayon crosstalk curl DBI dbplyr DelayedArray digest dplyr DT evaluate fansi fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GenomicScores glue GO.db graph HDF5Array highr hms Homo.sapiens htmltools htmlwidgets httpuv httr httr2 IRanges jquerylib jsonlite KEGGREST knitr lambda.r later lattice lazyeval lifecycle MafDb.1Kgenomes.phase3.hs37d5 MafDb.ExAC.r1.0.hs37d5 MafDb.gnomADex.r2.1.hs37d5 magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme openssl openxlsx org.Hs.eg.db OrganismDbi pillar pixmap pkgconfig plogr png PolyPhen.Hsapiens.dbSNP131 prettyunits progress promises purrr R6 rappdirs RBGL Rcpp RcppArmadillo RCurl rentrez restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass segmented seqinr shiny shinyjs SIFT.Hsapiens.dbSNP137 snow SNPlocs.Hsapiens.dbSNP144.GRCh37 sourcetools sp SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex TxDb.Hsapiens.UCSC.hg19.knownGene txdbmaker UCSC.utils utf8 VariantAnnotation vctrs withr xfun XML xml2 xtable XtraSNPlocs.Hsapiens.dbSNP144.GRCh37 XVector yaml zip zlibbioc

Using appreci8R

Rendered fromappreci8R.Rnwusingutils::Sweaveon Jun 24 2024.

Last update: 2020-12-02
Started: 2018-06-29

Citation

Development and contributors

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