CTexploreR
Explores Cancer Testis Genes
Bioconductor version: 3.23 · Package version: 1.8.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CTexploreR")Details
| Maintainer | Axelle Loriot <axelle.loriot@uclouvain.be> |
| Author | Axelle Loriot [aut, cre] (ORCID: <https://orcid.org/0000-0002-5288-8561>), Julie Devis [aut] (ORCID: <https://orcid.org/0000-0001-5525-5666>), Anna Diacofotaki [ctb], Charles De Smet [ths], Laurent Gatto [aut, ths] (ORCID: <https://orcid.org/0000-0002-1520-2268>) |
| License | Artistic-2.0 |
| URL | https://github.com/UCLouvain-CBIO/CTexploreR |
| Bug Reports | https://github.com/UCLouvain-CBIO/CTexploreR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DataImport, DifferentialExpression, Epigenetics, ExperimentHubSoftware, GeneExpression, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/CTexploreR/ |
Citation
From within R, enter citation("CTexploreR"):
Axelle Loriot, Julie Devis, Laurent Gatto. CTexploreR: Explores Cancer Testis Genes. doi:10.18129/B9.bioc.CTexploreR, R package version 1.8.0, https://bioconductor.org/packages/CTexploreR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | CTexploreR_1.8.0.tar.gz |
| Windows binary (x86_64) | CTexploreR_1.8.0.zip |
| macOS binary (arm64) | CTexploreR_1.8.0.tgz |
| macOS binary (x86_64) | CTexploreR_1.8.0.tgz |
Dependencies
Depends: R (>= 4.3), CTdata (>= 1.5.3)
Imports: BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment, GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), InteractiveComplexHeatmap