CTexploreR

Explores Cancer Testis Genes

Bioconductor version: 3.23 · Package version: 1.8.0

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
Downloads rank	376
Source branch	RELEASE_3_23
biocViews	DNAMethylation, DataImport, DifferentialExpression, Epigenetics, ExperimentHubSoftware, GeneExpression, Software, Transcriptomics

Documentation

Cancer Testis explorer

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