Package: seqCAT 1.35.0

Erik Fasterius

seqCAT: High Throughput Sequencing Cell Authentication Toolkit

The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours.

Authors:Erik Fasterius [aut, cre]

seqCAT_1.35.0.tar.gz
seqCAT_1.35.0.zip(r-4.7)seqCAT_1.35.0.zip(r-4.6)seqCAT_1.35.0.zip(r-4.5)
seqCAT_1.35.0.tgz(r-4.6-any)seqCAT_1.35.0.tgz(r-4.5-any)
seqCAT_1.35.0.tar.gz(r-4.7-any)seqCAT_1.35.0.tar.gz(r-4.6-any)
seqCAT_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
seqCAT/json (API)
NEWS

# Install 'seqCAT' in R:
install.packages('seqCAT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:seqCAT-1.35.0(bioc 3.24)seqCAT-1.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

coveragegenomicvariationsequencingvariantannotation

4.00 score 4 scripts 423 downloads 17 exports 91 dependencies

Last updated from:edfcad580e. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING176
linux-devel-x86_64NOTE404
source / vignettesOK316
linux-release-x86_64NOTE410
macos-release-arm64NOTE259
macos-oldrel-arm64NOTE253
windows-develNOTE336
windows-releaseNOTE348
windows-oldrelNOTE331
wasm-releaseOK158

Exports:calculate_similaritycompare_manycompare_profilescreate_profilecreate_profilesfilter_duplicatesfilter_variantslist_cosmiclist_variantsplot_heatmapplot_impactsplot_variant_listread_cosmicread_profileread_profileswrite_profilewrite_profiles

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryaml

seqCAT: The High Throughput Sequencing Cell Authentication Toolkit

Erik Fasterius

Rendered fromseqCAT.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2019-06-20
Started: 2017-08-31