How to Install and Uninstall berkeley-express Package on Ubuntu 16.04 LTS (Xenial Xerus)

Last updated: May 20,2024

1. Install "berkeley-express" package

Please follow the guidelines below to install berkeley-express on Ubuntu 16.04 LTS (Xenial Xerus)


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

Learn how to uninstall berkeley-express on Ubuntu 16.04 LTS (Xenial Xerus):


    
        
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                sudo apt remove
            
                        
                berkeley-express
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the berkeley-express package on Ubuntu 16.04 LTS (Xenial Xerus)

Package: berkeley-express
Priority: optional
Section: universe/science
Installed-Size: 2243
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Architecture: amd64
Version: 1.5.1-1
Depends: libbamtools2.4.0, libc6 (>= 2.17), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 5.2)
Recommends: med-config (>= 2.1)
Filename: pool/universe/b/berkeley-express/berkeley-express_1.5.1-1_amd64.deb
Size: 646096
MD5sum: 80bc88a0fa08ae1a8b65a3b6af0bd3a6
SHA1: f9b4c00ed49a48d1c7ff0c8549d8625698f9d244
SHA256: a52998cbb98b55484175a593ad65cfb0f0fc0769abbaccd0755810e5c00b026e
Description-en: Streaming quantification for high-throughput sequencing
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: 4d4c6aaf75f2e0fff660b1816f1f13c6
Homepage: http://bio.math.berkeley.edu/eXpress/index.html
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Origin: Ubuntu