How to Install and Uninstall berkeley-express-doc Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: November 26,2024

1. Install "berkeley-express-doc" package

Please follow the step by step instructions below to install berkeley-express-doc on Ubuntu 20.10 (Groovy Gorilla)


    
        
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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

Please follow the guidelines below to uninstall berkeley-express-doc on Ubuntu 20.10 (Groovy Gorilla):


    
        
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                sudo apt remove
            
                        
                berkeley-express-doc
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
    Copied

3. Information about the berkeley-express-doc package on Ubuntu 20.10 (Groovy Gorilla)

Package: berkeley-express-doc
Architecture: all
Version: 1.5.3+dfsg-1build3
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-1build3_all.deb
Size: 706472
MD5sum: 98d0b9c10056950f5db2538888c84f7f
SHA1: ff335af5ff6a0328f9d0d08abe6cc65228d747df
SHA256: 6c519e83f99d2e47d4de65ff832b2f922ee5358a358e5899397f8ab53caaeb38
SHA512: 5a9e06a1c81b87597ad9ae31ca854b524564f379d4edb06a49cc50bf111b5bb18e1be0b2a054b9b4cfa4616205dbe2793f32aaa591bf19f6d083127d7556946d
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