Package: CINdex 1.35.0
Yuriy Gusev
CINdex: Chromosome Instability Index
The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.
Authors:
CINdex_1.35.0.tar.gz
CINdex_1.35.0.zip(r-4.5)CINdex_1.35.0.zip(r-4.4)CINdex_1.35.0.zip(r-4.3)
CINdex_1.35.0.tgz(r-4.4-any)CINdex_1.35.0.tgz(r-4.3-any)
CINdex_1.35.0.tar.gz(r-4.5-noble)CINdex_1.35.0.tar.gz(r-4.4-noble)
CINdex_1.35.0.tgz(r-4.4-emscripten)CINdex_1.35.0.tgz(r-4.3-emscripten)
CINdex.pdf |CINdex.html✨
CINdex/json (API)
NEWS
| # Install 'CINdex' in R: |
| install.packages('CINdex', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- clin.crc - Colon cancer clinical dataset
- cnvgr.18.auto - Probe annotation file for Affymetrix Genome Wide Human SNP Array 6.0
- cyto.cin4heatmap - Cytoband CIN T-test output
- cytobands.cin - Cytoband CIN dataset
- geneAnno - CDS gene annotation file
- grl.data - Output of segmentation algorithm
- hg18.ucsctrack - Human reference annotation file
- snpgr.18.auto - Probe annotation file for Affymetrix Genome Wide Human SNP Array 6.0
On BioConductor:CINdex-1.33.0(bioc 3.20)CINdex-1.32.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwarecopynumbervariationgenomicvariationacghmicroarraygeneticssequencing
Last updated 23 days agofrom:5f3d72a4a0. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | WARNING | Oct 30 2024 |
| R-4.5-linux | WARNING | Oct 30 2024 |
| R-4.4-win | WARNING | Oct 30 2024 |
| R-4.4-mac | WARNING | Oct 30 2024 |
| R-4.3-win | WARNING | Oct 30 2024 |
| R-4.3-mac | WARNING | Oct 30 2024 |
Exports:comp.heatmapextract.genes.in.cyto.regionsrun.cin.chrrun.cin.cytottest.cyto.cin.heatmap
Dependencies:askpassBiocGenericsbitopscaToolsclicurldplyrfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluegplotsgridExtragtablegtoolshttrIRangesjsonliteKernSmoothlifecyclemagrittrmimeopensslpillarpkgconfigpngR6rlangS4VectorssomstringistringrsystibbletidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc
CINdex Tutorial
Rendered fromCINdex.Rnwusingknitr::knitron Oct 30 2024.Last update: 2018-09-06
Started: 2016-03-29
How to obtain Cytoband and Stain Information
Rendered fromHowToDownloadCytobandInfo.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2021-02-26
Started: 2021-02-26
Prepare input data for CINdex
Rendered fromPrepareInputData.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2021-02-27
Started: 2016-03-29
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Colon cancer clinical dataset | clin.crc |
| Probe annotation file for Affymetrix Genome Wide Human SNP Array 6.0 | cnvgr.18.auto |
| A comprehensive heatmap function that plots Chromosome and Cytoband heatmaps | comp.heatmap |
| Cytoband CIN T-test output | cyto.cin4heatmap |
| Cytoband CIN dataset | cytobands.cin |
| Given an input of cytobands, it outputs a list of genes that are present in the cytoband regions | extract.genes.in.cyto.regions |
| CDS gene annotation file | geneAnno |
| Output of segmentation algorithm | grl.data |
| Human reference annotation file | hg18.ucsctrack |
| Calculate chromosome CIN | run.cin.chr |
| Calculate cytoband CIN | run.cin.cyto |
| Probe annotation file for Affymetrix Genome Wide Human SNP Array 6.0 | snpgr.18.auto |
| Performs T test on cytoband level CIN data, and plots heatmap | ttest.cyto.cin.heatmap |
