Package: katdetectr 1.7.0

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]

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katdetectr.pdf |katdetectr.html✨
katdetectr/json (API)
NEWS

# 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-1.7.0(bioc 3.20)katdetectr-1.6.0(bioc 3.19)

wholegenome software snp sequencing classification variantannotation

8 exports 5 stars 5.40 score 118 dependencies 4 scripts 114 downloads

Last updated 5 months agofrom:c0e0cc78a6. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 20 2024
R-4.5-win	OK	Sep 19 2024
R-4.5-linux	OK	Sep 20 2024
R-4.4-win	OK	Sep 21 2024
R-4.4-mac	OK	Sep 20 2024
R-4.3-win	OK	Sep 20 2024
R-4.3-mac	OK	Jun 30 2024

Exports:constructKatdetect detectKataegis generateSyntheticData getGenomicVariants getInfo getKataegisFoci getSegments rainfallPlot

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

Overview of katdetectr

Daan Hazelaar and Job van Riet

Rendered fromGeneral_overview.Rmdusingknitr::rmarkdownon Sep 20 2024.

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