Package: katdetectr 1.15.0

Daan Hazelaar

katdetectr: Detection, Characterization and Visualization of Kataegis in Sequencing Data

Kataegis refers to the occurrence of regional hypermutation and is a phenomenon observed in a wide range of malignancies. Using changepoint detection katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants. Katdetectr has shown to be a robust package for the detection, characterization and visualization of kataegis.

Authors:Daan Hazelaar [aut, cre], Job van Riet [aut], Harmen van de Werken [ths]

katdetectr_1.15.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
katdetectr/json (API)

# Install 'katdetectr' in R:

install.packages('katdetectr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/erasmusmc-ccbc/katdetectr/issues

On BioConductor:katdetectr-1.15.0(bioc 3.24)katdetectr-1.14.0(bioc 3.23)

wholegenome software snp sequencing classification variantannotation

5.00 score 5 stars 4 scripts 274 downloads 8 exports 115 dependencies

Last updated from:b2135a5276. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	326
linux-devel-x86_64	NOTE	541
source / vignettes	OK	444
linux-release-x86_64	NOTE	540
macos-release-arm64	NOTE	399
macos-oldrel-arm64	NOTE	340
windows-devel	NOTE	444
windows-release	NOTE	384
windows-oldrel	NOTE	487
wasm-release	OK	289

Exports:constructKatdetect detectKataegis generateSyntheticData getGenomicVariants getInfo getKataegisFoci getSegments rainfallPlot

Dependencies:abind AnnotationDbi askpass backports BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg19 BSgenome.Hsapiens.UCSC.hg38 cachem changepoint changepoint.np checkmate cigarillo cli codetools commonmark cpp11 crayon curl data.table DBI DelayedArray DNAcopy dplyr farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggtext glue gridtext gtable httr IRanges isoband jpeg jsonlite KEGGREST labeling lambda.r lattice lifecycle litedown maftools magrittr markdown Matrix MatrixGenerics matrixStats memoise mime openssl pheatmap pillar pkgconfig plyranges png purrr R6 rbibutils RColorBrewer Rcpp RCurl Rdpack restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 XVector yaml zoo

Overview of katdetectr

Rendered fromGeneral_overview.Rmdusingknitr::rmarkdown

Last update: 2024-02-14
Started: 2022-05-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
constructKatdetect	constructKatdetect
detectKataegis	detectKataegis
Generate genomic variants with pre-defined kataegis foci.	generateSyntheticData
Retrieve genomic variants from KatDetect object.	getGenomicVariants getGenomicVariants,KatDetect-method
Retrieve model parameters from a KatDetect object.	getInfo getInfo,KatDetect-method
Retrieve kateagis foci from a KatDetect object.	getKataegisFoci getKataegisFoci,KatDetect-method
Retrieve segments from KatDetect a object.	getSegments getSegments,KatDetect-method
KatDetect-class: KatDetect objects	KatDetect-class
Katdetectr: A package for kataegis detection, characterization and visualization	katdetectr
Rainfall plot.	rainfallPlot