How To Install berkeley-express-doc on Debian 12
Introduction
In this tutorial we learn how to install berkeley-express-doc on Debian 12.
What is berkeley-express-doc
berkeley-express-doc is:
This package provides a PDF with the documentation for eXpress.
eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk.
In an analysis of the performance of eXpress for RNA-Seq data, it was observed that this efficiency does not come at a cost of accuracy. eXpress is more accurate than other available tools, even when limited to smaller datasets that do not require such efficiency. Moreover, like the Cufflinks program, eXpress can be used to estimate transcript abundances in multi-isoform genes. eXpress is also able to resolve multi-mappings of reads across gene families, and does not require a reference genome so that it can be used in conjunction with de novo assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model is based on previously described probabilistic models developed for RNA-Seq but is applicable to other settings where target sequences are sampled, and includes parameters for fragment length distributions, errors in reads, and sequence-specific fragment bias.
eXpress can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. The only required inputs to eXpress are a set of target sequences and a set of sequenced fragments multiply-aligned to them. While these target sequences will often be gene isoforms, they need not be. Haplotypes can be used as the reference for allele-specific expression analysis, binding regions for ChIP-Seq, or target genomes in metagenomics experiments. eXpress is useful in any analysis where reads multi-map to sequences that differ in abundance.
There are three methods to install berkeley-express-doc on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install berkeley-express-doc Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install berkeley-express-doc using apt-get by running the following command:
sudo apt-get -y install berkeley-express-doc
Install berkeley-express-doc Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install berkeley-express-doc using apt by running the following command:
sudo apt -y install berkeley-express-doc
Install berkeley-express-doc 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 berkeley-express-doc using aptitude by running the following command:
sudo aptitude -y install berkeley-express-doc
How To Uninstall berkeley-express-doc on Debian 12
To uninstall only the berkeley-express-doc package we can use the following command:
sudo apt-get remove berkeley-express-doc
Uninstall berkeley-express-doc And Its Dependencies
To uninstall berkeley-express-doc and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove berkeley-express-doc
Remove berkeley-express-doc Configurations and Data
To remove berkeley-express-doc configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge berkeley-express-doc
Remove berkeley-express-doc configuration, data, and all of its dependencies
We can use the following command to remove berkeley-express-doc configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge berkeley-express-doc
Dependencies
berkeley-express-doc have the following dependencies:
References
Summary
In this tutorial we learn how to install berkeley-express-doc package on Debian 12 using different package management tools: apt, apt-get and aptitude.