Package: iCNV 1.27.0
Zilu Zhou
iCNV: Integrated Copy Number Variation detection
Integrative copy number variation (CNV) detection from multiple platform and experimental design.
Authors:
iCNV_1.27.0.tar.gz
iCNV_1.27.0.zip(r-4.5)iCNV_1.27.0.zip(r-4.4)iCNV_1.27.0.zip(r-4.3)
iCNV_1.27.0.tgz(r-4.4-any)iCNV_1.27.0.tgz(r-4.3-any)
iCNV_1.27.0.tar.gz(r-4.5-noble)iCNV_1.27.0.tar.gz(r-4.4-noble)
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iCNV.pdf |iCNV.html✨
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-1.27.0(bioc 3.21)iCNV-1.26.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyexomeseqwholegenomesnpcopynumbervariationhiddenmarkovmodel
Last updated 2 months agofrom:3beaddb042. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 24 2024 |
| R-4.5-win | WARNING | Nov 24 2024 |
| R-4.5-linux | WARNING | Dec 24 2024 |
| R-4.4-win | WARNING | Nov 24 2024 |
| R-4.4-mac | WARNING | Dec 24 2024 |
| R-4.3-win | WARNING | Nov 24 2024 |
| R-4.3-mac | WARNING | Dec 24 2024 |
Exports:bambaf_from_vcfbed_generatorget_array_inputiCNV_detectionicnv_output_to_gboutput_listplot_intensityplotHMMscoreplotindi
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeBSgenome.Hsapiens.UCSC.hg19clicodetoolsCODEXcolorspacecpp11crayoncurldata.tableDelayedArraydotCall64dplyrfansifarverfieldsformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpurrrR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowspamSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttruncnormUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc
