How to Install and Uninstall berkeley-express-doc Package on Ubuntu 21.04 (Hirsute Hippo)

Last updated: May 19,2024

1. Install "berkeley-express-doc" package

Please follow the instructions below to install berkeley-express-doc on Ubuntu 21.04 (Hirsute Hippo)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                berkeley-express-doc
            
                    
    
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2. Uninstall "berkeley-express-doc" package

This tutorial shows how to uninstall berkeley-express-doc on Ubuntu 21.04 (Hirsute Hippo):


    
        
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                sudo apt remove
            
                        
                berkeley-express-doc
            
                    
    
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            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the berkeley-express-doc package on Ubuntu 21.04 (Hirsute Hippo)

Package: berkeley-express-doc
Architecture: all
Version: 1.5.3+dfsg-1build4
Multi-Arch: foreign
Priority: optional
Section: universe/doc
Source: berkeley-express
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 3249
Filename: pool/universe/b/berkeley-express/berkeley-express-doc_1.5.3+dfsg-1build4_all.deb
Size: 706560
MD5sum: 4db9658ac500969bf71f4ce9f920cc36
SHA1: 1d88112aa59a0bac6f13acd7509a3176c6f831b9
SHA256: 5b13a7a0470ecde6a898c1e07e3b3e39994d0fdd4e0b3c6c5ba09878df1f4551
SHA512: d93795e83cc730e7f8e9e70d205181901aebd6b2dab73df1178a8a1aaea0bab8ee61695e9e726b8198d95af689ad4c5984f77316df41c0f467b0ed09e93d9801
Homepage: http://bio.math.berkeley.edu/eXpress/index.html
Description-en: Documentation for RNA-Seq tool eXpress
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.
Description-md5: 6872981809a9528fac787c2292ad040e