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:
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✨
card.svg |card.png
iCNV/json (API)
NEWS
| # Install 'iCNV' in R: |
| install.packages('iCNV', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- 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.
immunooncologyexomeseqwholegenomesnpcopynumbervariationhiddenmarkovmodel
Last updated from:e9ed45a7d8. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 270 | ||
| linux-devel-x86_64 | WARNING | 494 | ||
| source / vignettes | OK | 355 | ||
| linux-release-x86_64 | WARNING | 486 | ||
| macos-release-arm64 | WARNING | 261 | ||
| macos-oldrel-arm64 | WARNING | 228 | ||
| windows-devel | WARNING | 722 | ||
| windows-release | WARNING | 671 | ||
| windows-oldrel | WARNING | 740 | ||
| wasm-release | OK | 224 |
Exports:bambaf_from_vcfbed_generatorget_array_inputiCNV_detectionicnv_output_to_gboutput_listplot_intensityplotHMMscoreplotindi
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeBSgenome.Hsapiens.UCSC.hg19cigarilloclicodetoolsCODEXcpp11crayoncurldata.tableDelayedArraydotCall64dplyrfarverfieldsformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrmapsMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpurrrR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowspamSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttruncnormUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml
