How To Install r-bioc-tfbstools on Debian 10
Introduction
In this tutorial we learn how to install r-bioc-tfbstools on Debian 10.
What is r-bioc-tfbstools
r-bioc-tfbstools is:
TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.
There are three methods to install r-bioc-tfbstools on Debian 10. 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-tfbstools Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install r-bioc-tfbstools using apt-get by running the following command:
sudo apt-get -y install r-bioc-tfbstools
Install r-bioc-tfbstools Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-tfbstools using apt by running the following command:
sudo apt -y install r-bioc-tfbstools
Install r-bioc-tfbstools 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.
sudo aptitude update
After updating apt database, We can install r-bioc-tfbstools using aptitude by running the following command:
sudo aptitude -y install r-bioc-tfbstools
How To Uninstall r-bioc-tfbstools on Debian 10
To uninstall only the r-bioc-tfbstools package we can use the following command:
sudo apt-get remove r-bioc-tfbstools
Uninstall r-bioc-tfbstools And Its Dependencies
To uninstall r-bioc-tfbstools and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove r-bioc-tfbstools
Remove r-bioc-tfbstools Configurations and Data
To remove r-bioc-tfbstools configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge r-bioc-tfbstools
Remove r-bioc-tfbstools configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-tfbstools configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-tfbstools
Dependencies
r-bioc-tfbstools have the following dependencies:
- r-base-core
- r-api-3.5
- r-bioc-biobase
- r-bioc-biostrings
- r-bioc-biocgenerics
- r-bioc-biocparallel
- r-bioc-bsgenome
- r-cran-catools
- r-bioc-cner
- r-bioc-dirichletmultinomial
- r-bioc-genomeinfodb
- r-bioc-genomicranges
- r-cran-gtools
- r-bioc-iranges
- r-cran-dbi
- r-cran-rsqlite
- r-bioc-rtracklayer
- r-bioc-seqlogo
- r-bioc-s4vectors
- r-cran-tfmpvalue
- r-cran-xml
- r-bioc-xvector
- libc6
References
Summary
In this tutorial we learn how to install r-bioc-tfbstools package on Debian 10 using different package management tools: apt, apt-get and aptitude.