Package: iCNV 1.33.0

Zilu Zhou

iCNV: Integrated Copy Number Variation detection

Integrative copy number variation (CNV) detection from multiple platform and experimental design.

Authors:Zilu Zhou, Nancy Zhang

iCNV_1.33.0.tar.gz
iCNV_1.33.0.zip(r-4.7)iCNV_1.33.0.zip(r-4.6)iCNV_1.33.0.zip(r-4.5)
iCNV_1.33.0.tgz(r-4.6-any)iCNV_1.33.0.tgz(r-4.5-any)
iCNV_1.33.0.tar.gz(r-4.7-any)iCNV_1.33.0.tar.gz(r-4.6-any)
iCNV_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iCNV/json (API)

# Install 'iCNV' in R:

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

Datasets:

filenm - Name of the file
icnv_res0 - Example iCNV calling results.
ngs_baf - BAF list from NGS
ngs_baf.chr - BAF chromosome from NGS
ngs_baf.id - BAF variants id from NGS
ngs_baf.nm - BAF variants sample name from NGS
ngs_baf.pos - BAF position list from NGS
ngs_plr - Normalized Poisson likelihood ratio list from NGS
ngs_plr.pos - Exon location list from NGS
normObj - Demo data pre-stored for normObj.
qcObj - Demo data pre-stored for qcObj.
sampname - CODEX sample name
sampname_qc - QCed sample name
snp_baf - BAF list from Array
snp_baf.pos - BAF position list from Array
snp_lrr - Normalized log R ratio list from Array
snp_lrr.pos - SNP position list from Array

On BioConductor:iCNV-1.33.0(bioc 3.24)iCNV-1.32.0(bioc 3.23)

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

immunooncology exomeseq wholegenome snp copynumbervariation hiddenmarkovmodel

4.30 score 6 scripts 2 mentions 9 exports 87 dependencies

Last updated from:e9ed45a7d8. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	265
linux-devel-x86_64	WARNING	453
source / vignettes	OK	375
linux-release-x86_64	WARNING	446
macos-release-arm64	WARNING	220
macos-oldrel-arm64	WARNING	316
windows-devel	WARNING	620
windows-release	WARNING	654
windows-oldrel	WARNING	625
wasm-release	OK	204

Exports:bambaf_from_vcf bed_generator get_array_input iCNV_detection icnv_output_to_gb output_list plot_intensity plotHMMscore plotindi

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome BSgenome.Hsapiens.UCSC.hg19 cigarillo cli codetools CODEX cpp11 crayon curl data.table DelayedArray dotCall64 dplyr farver fields formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr maps Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig purrr R6 RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow spam SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect truncnorm UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml

Maintainer | 1. Website and online forum | 2. iCNV workflow | 2.1 Install iCNV. | 2.2 .bam file normalization using CODEX | 2.3 sequence variants BAF calling | 2.4 SNP array LRR normalization and BAF | 2.5 Mutiple platform CNV detection using iCNV | 2.6 Single platform CNV detection using iCNV | 3. Session information

Rendered fromiCNV-vignette.Rmdusingknitr::rmarkdown

Last update: 2018-08-30
Started: 2017-09-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get BAM baf information from vcf	bambaf_from_vcf
Generate BED file for WGS dataset.	bed_generator
chromosome of the example	chr
Name of the file	filenm
Get array information from given format	get_array_input
CNV detection	iCNV_detection
Convert icnv.output to input for Genome Browser.	icnv_output_to_gb
Example iCNV calling results.	icnv_res0
BAF list from NGS	ngs_baf
BAF chromosome from NGS	ngs_baf.chr
BAF variants id from NGS	ngs_baf.id
BAF variants sample name from NGS	ngs_baf.nm
BAF position list from NGS	ngs_baf.pos
Normalized Poisson likelihood ratio list from NGS	ngs_plr
Exon location list from NGS	ngs_plr.pos
Demo data pre-stored for normObj.	normObj
Generate ouput list.	output_list
plot out the NGS plr or array lrr.	plot_intensity
Plot CNV inference score.	plotHMMscore
Individual sample plot	plotindi
name of project	projname
Demo data pre-stored for qcObj.	qcObj
CODEX sample name	sampname
QCed sample name	sampname_qc
BAF list from Array	snp_baf
BAF position list from Array	snp_baf.pos
Normalized log R ratio list from Array	snp_lrr
SNP position list from Array	snp_lrr.pos

Usage by other packages (reverse dependencies)