Package: CNVfilteR 1.21.0

Jose Marcos Moreno-Cabrera

CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls

CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.

Authors:Jose Marcos Moreno-Cabrera [aut, cre], Bernat Gel [aut]

CNVfilteR_1.21.0.tar.gz
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CNVfilteR.pdf |CNVfilteR.html✨
CNVfilteR/json (API)
NEWS

# Install 'CNVfilteR' in R:

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

Bug tracker:https://github.com/jpuntomarcos/cnvfilter/issues

On BioConductor:CNVfilteR-1.21.0(bioc 3.21)CNVfilteR-1.20.0(bioc 3.20)

copynumbervariation sequencing dnaseq visualization dataimport

5.18 score 5 stars 1 scripts 246 downloads 7 exports 139 dependencies

Last updated 5 months agofrom:b987028fd2. Checks:3 OK, 3 ERROR, 3 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 29 2025
R-4.5-win	ERROR	Mar 29 2025
R-4.5-mac	ERROR	Mar 29 2025
R-4.5-linux	ERROR	Mar 29 2025
R-4.4-win	NOTE	Mar 29 2025
R-4.4-mac	NOTE	Mar 29 2025
R-4.4-linux	NOTE	Mar 29 2025
R-4.3-win	OK	Mar 29 2025
R-4.3-mac	OK	Mar 29 2025

Exports:filterCNVs loadCNVcalls loadSNPsFromVCF loadVCFs plotAllCNVs plotScoringModel plotVariantsForCNV

Dependencies:abind AnnotationDbi AnnotationFilter askpass assertthat backports bamsignals base64enc bezier BH Biobase BiocGenerics BiocIO BiocParallel Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster cn.mops codetools colorspace CopyNumberPlots cpp11 crayon curl data.table DBI DelayedArray dichromat digest ensembldb evaluate fansi farver fastmap fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite karyoploteR KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png pracma ProtGenerics R6 rappdirs RColorBrewer Rcpp RCurl regioneR restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML XVector yaml zlibbioc

CNVfilteR: Remove false positives of CNV calling tools by using SNV calls

Jose Marcos Moreno-Cabrera [email protected] and Bernat Gel [email protected]

Rendered fromCNVfilteR.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2022-12-02
Started: 2019-10-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
auxAddCNcolumn	auxAddCNcolumn
auxGetVcfSource	auxGetVcfSource
auxProcessVariants	auxProcessVariants
filterCNVs	filterCNVs
getVariantScore	getVariantScore
loadCNVcalls	loadCNVcalls
loadSNPsFromVCF	loadSNPsFromVCF
loadVCFs	loadVCFs
plotAllCNVs	plotAllCNVs
plotVariantsForCNV	plotScoringModel
plotVariantsForCNV	plotVariantsForCNV