How to Install and Uninstall tnseq-transit Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: January 11,2025

1. Install "tnseq-transit" package

This tutorial shows how to install tnseq-transit on Ubuntu 20.10 (Groovy Gorilla)


    
        
            $
        

        
            
                sudo apt update
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt install
            
                        
                tnseq-transit
            
                    
    
    Copied

2. Uninstall "tnseq-transit" package

Please follow the step by step instructions below to uninstall tnseq-transit on Ubuntu 20.10 (Groovy Gorilla):


    
        
            $
        

        
            
                sudo apt remove
            
                        
                tnseq-transit
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
    Copied

3. Information about the tnseq-transit package on Ubuntu 20.10 (Groovy Gorilla)

Package: tnseq-transit
Architecture: amd64
Version: 3.1.0-2
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: 41309
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_3.1.0-2_amd64.deb
Size: 6912980
MD5sum: a5b64c10c35ab11db1cccf7a0ffd168e
SHA1: 6816491c2fc1335a00dfc376e960854e06202efb
SHA256: 93de6f4f571b92b3beb114861978675318fb47504d4b8a9c87a0d3e163aa62e5
SHA512: 5ae56849034cfbae4b50a4479694b781c074cc90125207a5d0de7af1e2d1a04c8091d2e38c1b7c0601d120af3a581f67989d023ebcaece9f75a6dfb4cfec337a
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