How To Install pscan-chip on Ubuntu 22.04
Introduction
In this tutorial we learn how to install pscan-chip
on Ubuntu 22.04.
What is pscan-chip
pscan-chip is:
Regulation of transcription is one of the main check points of gene expression regulation and plays a key role in fundamental processes like cellular differentiation and dynamic molecular responses to stimuli The transcriptional activity of genes is finely regulated by the interaction of sequence elements on the DNA (transcription factor binding sites or TFBSs) and particular proteins called Transcription Factors (TFs). , TFBSs are usually clustered in specific regulatory genomic regions called promoters and enhancers. TFs usually recognize TFBSs in a loose sequence specific fashion but there is no computational way to determine if any given sequence motif on the DNA is actually bound in-vivo by a TF, even when the motif is an istance of the sequences typically bound by the TF itself.
Tools like Pscan and PscanChIP analyse a set of regulatory sequences to detect motif enrichment. The rationale is that if a given TFBS is present in a “surpisingly high” number of istances then there is a good chance that the TF that recognize that motif is a common regulator of the input sequences, thus they use redundancy as an information source.
While Pscan (of the pscan-tfbs package) is tailored to work on promoters, that is the regulatory regions upstream of transcription start sites, PscanChIP is suited to work on more general regulatory genomic regions like the ones identified through ChIP-Seq experiments.
There are three methods to install pscan-chip
on Ubuntu 22.04. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install pscan-chip Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install pscan-chip
using apt-get
by running the following command:
sudo apt-get -y install pscan-chip
Install pscan-chip Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install pscan-chip
using apt
by running the following command:
sudo apt -y install pscan-chip
Install pscan-chip 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 pscan-chip
using aptitude
by running the following command:
sudo aptitude -y install pscan-chip
How To Uninstall pscan-chip on Ubuntu 22.04
To uninstall only the pscan-chip
package we can use the following command:
sudo apt-get remove pscan-chip
Uninstall pscan-chip And Its Dependencies
To uninstall pscan-chip
and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove pscan-chip
Remove pscan-chip Configurations and Data
To remove pscan-chip
configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge pscan-chip
Remove pscan-chip configuration, data, and all of its dependencies
We can use the following command to remove pscan-chip
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pscan-chip
References
Summary
In this tutorial we learn how to install pscan-chip
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.