How To Install r-cran-spp on Ubuntu 20.04
Introduction
In this tutorial we learn how to install r-cran-spp
on Ubuntu 20.04.
What is r-cran-spp
r-cran-spp is:
R package for anlaysis of ChIP-seq and other functional sequencing data
- Assess overall DNA-binding signals in the data and select appropriate quality of tag alignment.
- Discard or restrict positions with abnormally high number of tags.
- Calculate genome-wide profiles of smoothed tag density and save them in WIG files for viewing in other browsers.
- Calculate genome-wide profiles providing conservative statistical estimates of fold enrichment ratios along the genome. These can be exported for browser viewing, or thresholded to determine regions of significant enrichment/depletion.
- Determine statistically significant point binding positions
- Assess whether the set of point binding positions detected at a current sequencing depth meets saturation criteria, and if does not, estimate what sequencing depth would be required to do so.
There are three methods to install r-cran-spp
on Ubuntu 20.04. 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-cran-spp 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-cran-spp
using apt-get
by running the following command:
sudo apt-get -y install r-cran-spp
Install r-cran-spp Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install r-cran-spp
using apt
by running the following command:
sudo apt -y install r-cran-spp
Install r-cran-spp 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 Ubuntu. Update apt database with aptitude
using the following command.
sudo aptitude update
After updating apt database, We can install r-cran-spp
using aptitude
by running the following command:
sudo aptitude -y install r-cran-spp
How To Uninstall r-cran-spp on Ubuntu 20.04
To uninstall only the r-cran-spp
package we can use the following command:
sudo apt-get remove r-cran-spp
Uninstall r-cran-spp And Its Dependencies
To uninstall r-cran-spp
and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove r-cran-spp
Remove r-cran-spp Configurations and Data
To remove r-cran-spp
configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge r-cran-spp
Remove r-cran-spp configuration, data, and all of its dependencies
We can use the following command to remove r-cran-spp
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-cran-spp
References
Summary
In this tutorial we learn how to install r-cran-spp
package on Ubuntu 20.04 using different package management tools: apt
, apt-get
and aptitude
.