CTexploreR
Explores Cancer Testis Genes
Bioconductor version: Release (3.19)
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.
Author: Axelle Loriot [aut, cre] 
, Julie Devis [aut] , Anna Diacofotaki [ctb], Charles De Smet [ths], Laurent Gatto [aut, ths]
Maintainer: Axelle Loriot <axelle.loriot at uclouvain.be>
citation("CTexploreR")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CTexploreR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CTexploreR")| Cancer Testis Explorer | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DataImport, DifferentialExpression, Epigenetics, ExperimentHubSoftware, GeneExpression, Software, Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (< 6 months) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3), CTdata |
| Imports | BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment, GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics |
| System Requirements | |
| URL | https://github.com/UCLouvain-CBIO/CTexploreR |
| Bug Reports | https://github.com/UCLouvain-CBIO/CTexploreR/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CTexploreR_1.0.0.tar.gz |
| Windows Binary (x86_64) | CTexploreR_1.0.0.zip |
| macOS Binary (x86_64) | CTexploreR_1.0.0.tgz |
| macOS Binary (arm64) | CTexploreR_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CTexploreR |
| Source Repository (Developer Access) | git clone [email protected]:packages/CTexploreR |
| Bioc Package Browser | https://code.bioconductor.org/browse/CTexploreR/ |
| Package Short Url | https://bioconductor.org/packages/CTexploreR/ |
| Package Downloads Report | Download Stats |