How To Install r-bioc-tcgabiolinks on Debian 11
Introduction
In this tutorial we learn how to install r-bioc-tcgabiolinks
on Debian 11.
What is r-bioc-tcgabiolinks
r-bioc-tcgabiolinks is:
The aim of TCGAbiolinks is:
- facilitate the GDC open-access data retrieval,
- prepare the data using the appropriate pre-processing strategies,
- provide the means to carry out different standard analyses and
- to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
There are three methods to install r-bioc-tcgabiolinks
on Debian 11. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install r-bioc-tcgabiolinks Using apt-get
Update apt database with apt-get
using the following command.
After updating apt database, We can install r-bioc-tcgabiolinks
using apt-get
by running the following command:
Install r-bioc-tcgabiolinks Using apt
Update apt database with apt
using the following command.
After updating apt database, We can install r-bioc-tcgabiolinks
using apt
by running the following command:
Install r-bioc-tcgabiolinks Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude
using the following command.
After updating apt database, We can install r-bioc-tcgabiolinks
using aptitude
by running the following command:
How To Uninstall r-bioc-tcgabiolinks on Debian 11
To uninstall only the r-bioc-tcgabiolinks
package we can use the following command:
Uninstall r-bioc-tcgabiolinks And Its Dependencies
To uninstall r-bioc-tcgabiolinks
and its dependencies that are no longer needed by Debian 11, we can use the command below:
Remove r-bioc-tcgabiolinks Configurations and Data
To remove r-bioc-tcgabiolinks
configuration and data from Debian 11 we can use the following command:
Remove r-bioc-tcgabiolinks configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-tcgabiolinks
configurations, data and all of its dependencies, we can use the following command:
Dependencies
r-bioc-tcgabiolinks have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.12
- r-cran-downloader
- r-bioc-biomart
- r-cran-dplyr
- r-cran-tibble
- r-bioc-genomicranges
- r-cran-xml
- r-cran-data.table
- r-cran-jsonlite
- r-cran-plyr
- r-cran-knitr
- r-cran-ggplot2
- r-cran-stringr
- r-bioc-iranges
- r-cran-rvest
- r-bioc-s4vectors
- r-cran-r.utils
- r-bioc-summarizedexperiment
- r-bioc-tcgabiolinksgui.data
- r-cran-readr
- r-cran-tidyr
- r-cran-purrr
- r-cran-xml2
- r-cran-httr
References
Summary
In this tutorial we learn how to install r-bioc-tcgabiolinks
package on Debian 11 using different package management tools: apt
, apt-get
and aptitude
.