How to Install and Uninstall tnseq-transit Package on Ubuntu 21.10 (Impish Indri)

Last updated: November 07,2024

1. Install "tnseq-transit" package

Please follow the guidance below to install tnseq-transit on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                tnseq-transit
            
                    
    
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2. Uninstall "tnseq-transit" package

Please follow the guidelines below to uninstall tnseq-transit on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                tnseq-transit
            
                    
    
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            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the tnseq-transit package on Ubuntu 21.10 (Impish Indri)

Package: tnseq-transit
Architecture: amd64
Version: 3.2.1-1
Priority: optional
Section: universe/science
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 76913
Provides: transit
Depends: python3-matplotlib, python3-numpy, python3-pil, python3-pkg-resources, python3-scipy, python3-statsmodels, python3:any, python3-pubsub, python3-wxgtk4.0, bwa
Breaks: transit
Replaces: transit
Filename: pool/universe/t/tnseq-transit/tnseq-transit_3.2.1-1_amd64.deb
Size: 8948112
MD5sum: 2c14d0e84f8a3a01e3d24432b67b560a
SHA1: e7400f389271693a8ad05f98ac8436456569aaad
SHA256: 2d00547e442916777426425267150cd1955f6af620bacd6f60f6af8b7ff3c346
SHA512: 548b68e9248c2a26f56ccb989ffe08010afac896f89d4e86d9ef997c2cd325b40c197426f8a2a1cfbd754be099e260019e82ca50add39c433ba00dc4300e3926
Homepage: http://saclab.tamu.edu/essentiality/transit/
Description-en: statistical calculations of essentiality of genes or genomic regions
This is a software that can be used to analyze Tn-Seq datasets. It
includes various statistical calculations of essentiality of genes or
genomic regions (including conditional essentiality between 2
conditions). These methods were developed and tested as a collaboration
between the Sassetti lab (UMass) and the Ioerger lab (Texas A&M)
.
TRANSIT is capable of analyzing TnSeq libraries constructed with Himar1
or Tn5 datasets.
.
TRANSIT assumes you have already done pre-processing of raw sequencing
files (.fastq) and extracted read counts into a .wig formatted file.
The .wig file should contain the counts at all sites where an insertion
could take place (including sites with no reads). For Himar1 datasets
this is all TA sites in the genome. For Tn5 datasets this would be all
nucleotides in the genome.
Description-md5: ed6ccc42fdb3924f7848894e28b09ade