Installation | General Workflow | Data Source | Gene expression | CNA | Custom reader function | Usage Example | Example Data Source | Sample Description Generation | Joint Gene Expression Table | Joint CNA Status Table Mapped onto Gene Locations | Parallelization | Read gene information directly from data | CNA-driven Differentially Expressed Genes Identification | Q and As | Q: Why required to use the bundled hg19 human genome reference?
Package: iGC 1.43.0
Liang-Bo Wang
iGC: An integrated analysis package of Gene expression and Copy number alteration
This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.
Authors:
iGC_1.43.0.tar.gz
iGC_1.43.0.zip(r-4.7)iGC_1.43.0.zip(r-4.6)iGC_1.43.0.zip(r-4.5)
iGC_1.43.0.tgz(r-4.6-any)iGC_1.43.0.tgz(r-4.5-any)
iGC_1.43.0.tar.gz(r-4.7-any)iGC_1.43.0.tar.gz(r-4.6-any)
iGC_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iGC/json (API)
| # Install 'iGC' in R: |
| install.packages('iGC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ccwang002/igc/issues
Datasets:
- hg19DBNM - Hg19-RefSeq
On BioConductor:iGC-1.43.0(bioc 3.24)iGC-1.42.0(bioc 3.23)
softwarebiological questiondifferentialexpressiongenomicvariationassaydomaincopynumbervariationgeneexpressionresearchfieldgeneticstechnologymicroarraysequencingworkflowstepmultiplecomparison
Last updated from:7cb644f3d4. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 187 | ||
| linux-devel-x86_64 | NOTE | 183 | ||
| source / vignettes | OK | 149 | ||
| linux-release-x86_64 | NOTE | 190 | ||
| macos-release-arm64 | NOTE | 86 | ||
| macos-oldrel-arm64 | NOTE | 85 | ||
| windows-devel | NOTE | 94 | ||
| windows-release | NOTE | 89 | ||
| windows-oldrel | NOTE | 77 | ||
| wasm-release | OK | 120 |
Exports:create_gene_cnacreate_gene_expcreate_sample_descdirect_gene_cnafind_cna_driven_gene
Dependencies:data.tableplyrRcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Load and map CNA gain/loss onto human gene location by genome reference | create_gene_cna |
| Create an joint gene expression table of all samples | create_gene_exp |
| Create sample description table containing all required inputs | create_sample_desc |
| Load the existed CNA gain/loss based on gene location. | direct_gene_cna |
| Perform an integrated analysis of gene expression (GE) and copy number alteration (CNA) | find_cna_driven_gene |
| hg19-RefSeq | hg19DBNM |
| iGC: an integrated analysis package of gene expression and copy number alteration | iGC-package iGC |