Introduction | Input file formats | The package functions | Plotting parameters
Package: OmicCircos 1.51.0
Ying Hu
OmicCircos: High-quality circular visualization of omics data
OmicCircos is an R application and package for generating high-quality circular plots for omics data.
Authors:
OmicCircos_1.51.0.tar.gz
OmicCircos_1.51.0.zip(r-4.7)OmicCircos_1.51.0.zip(r-4.6)OmicCircos_1.51.0.zip(r-4.5)
OmicCircos_1.51.0.tgz(r-4.6-any)OmicCircos_1.51.0.tgz(r-4.5-any)
OmicCircos_1.51.0.tar.gz(r-4.7-any)OmicCircos_1.51.0.tar.gz(r-4.6-any)
OmicCircos_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
OmicCircos/json (API)
| # Install 'OmicCircos' in R: |
| install.packages('OmicCircos', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- TCGA.BC_Her2_cnv_exp - TCGA BRCA expression and cnv association
- TCGA.BC.cnv.2k.60 - Copy number data of TCGA Breast Cancer
- TCGA.BC.fus - TCGA Breast Cancer gene fusion data.
- TCGA.BC.gene.exp.2k.60 - TCGA BRCA expression data
- TCGA.BC.sample60 - TCGA BRCA Sample names and subtypes
- TCGA.PAM50_genefu_hg18 - BRCA PAM50 gene list
- UCSC.chr.colors - Chromosome banding colors
- UCSC.hg18 - Human hg18 circumference coordinates
- UCSC.hg18.chr - Human hg18 segment data.
- UCSC.hg19 - Human hg19 circumference coordinates
- UCSC.hg19.chr - Human hg19 segment data
- UCSC.mm10 - Mouse mm10 circumference coordinates
- UCSC.mm10.chr - Mouse mm10 segment data.
- UCSC.mm9 - Mouse mm9 circumference coordinates
- UCSC.mm9.chr - Mouse mm9 segment data.
On BioConductor:OmicCircos-1.51.0(bioc 3.24)OmicCircos-1.50.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
visualizationstatisticsannotation
Last updated from:a702d55b6c. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 153 | ||
| linux-devel-x86_64 | WARNING | 213 | ||
| source / vignettes | OK | 213 | ||
| linux-release-x86_64 | WARNING | 165 | ||
| macos-release-arm64 | WARNING | 111 | ||
| macos-oldrel-arm64 | WARNING | 88 | ||
| windows-devel | WARNING | 116 | ||
| windows-release | WARNING | 118 | ||
| windows-oldrel | WARNING | 107 | ||
| wasm-release | OK | 100 |
Exports:circossegAnglePosim.circos
Dependencies:BiocGenericsgenericsGenomicRangesIRangesS4VectorsSeqinfo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| OmicCircos package | OmicCircos |
| draw circular | circos |
| generate circular skeleton data from user's mapping data | segAnglePo |
| ~~ Methods for Function 'segAnglePo' ~~ | segAnglePo,data.frame-method segAnglePo,GRanges-method segAnglePo-methods |
| circular data simulation | sim.circos |
| TCGA BRCA expression and cnv association | TCGA.BC_Her2_cnv_exp |
| copy number data of TCGA Breast Cancer | TCGA.BC.cnv.2k.60 |
| TCGA Breast Cancer gene fusion data. | TCGA.BC.fus |
| TCGA BRCA expression data | TCGA.BC.gene.exp.2k.60 |
| TCGA BRCA Sample names and subtypes | TCGA.BC.sample60 |
| BRCA PAM50 gene list (hg18) | TCGA.PAM50_genefu_hg18 |
| chromosome banding colors | UCSC.chr.colors |
| human hg18 circumference coordinates | UCSC.hg18 |
| human hg18 segment data. | UCSC.hg18.chr |
| human hg19 circumference coordinates | UCSC.hg19 |
| human hg19 segment data | UCSC.hg19.chr |
| mouse mm10 circumference coordinates | UCSC.mm10 |
| mouse mm10 segment data. | UCSC.mm10.chr |
| mouse mm9 circumference coordinates | UCSC.mm9 |
| mouse mm9 segment data. | UCSC.mm9.chr |
