How to Install and Uninstall r-cran-tigger Package on Ubuntu 21.10 (Impish Indri)

Last updated: November 07,2024

1. Install "r-cran-tigger" package

Please follow the instructions below to install r-cran-tigger on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                r-cran-tigger
            
                    
    
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2. Uninstall "r-cran-tigger" package

This tutorial shows how to uninstall r-cran-tigger on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                r-cran-tigger
            
                    
    
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            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the r-cran-tigger package on Ubuntu 21.10 (Impish Indri)

Package: r-cran-tigger
Architecture: all
Version: 1.0.0-1
Priority: optional
Section: universe/gnu-r
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian R Packages Maintainers
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 4169
Depends: r-base-core (>= 4.0.0.20200528-1), r-api-4.0, r-cran-ggplot2 (>= 3.2.0), r-cran-alakazam (>= 1.0.0), r-cran-shazam (>= 1.0.0), r-cran-dplyr (>= 0.8.1), r-cran-doparallel, r-cran-foreach, r-cran-gridextra, r-cran-gtools, r-cran-iterators, r-cran-lazyeval, r-cran-rlang, r-cran-stringi, r-cran-tidyr (>= 0.1.0)
Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat
Filename: pool/universe/r/r-cran-tigger/r-cran-tigger_1.0.0-1_all.deb
Size: 4119460
MD5sum: 157ef07a25eea5bc5d2903e5bb27c6b2
SHA1: 0b4f2aaafd1908c9070dc8f76ba11cddaee77f70
SHA256: 393db9436f97cf12e4bfe59d390f28917af8cda946724b2f03edbfe63d8f61fe
SHA512: 54786077076769b6d0cdf643703e9970c917b5106ab81d765c630faa3f72637cd9cfa0d97dde91c6c95b9eab444ef23abd217c078a680ed75d2a4c6cbb26e336
Homepage: https://cran.r-project.org/package=tigger
Description-en: Infers new Immunoglobulin alleles from Rep-Seq Data
Summary: Infers the V genotype of an individual from immunoglobulin (Ig)
repertoire-sequencing (Rep-Seq) data, including detection of any novel
alleles. This information is then used to correct existing V allele calls
from among the sample sequences.
.
High-throughput sequencing of B cell immunoglobulin receptors is
providing unprecedented insight into adaptive immunity. A key step in
analyzing these data involves assignment of the germline V, D and J gene
segment alleles that comprise each immunoglobulin sequence by matching
them against a database of known V(D)J alleles. However, this process
will fail for sequences that utilize previously undetected alleles,
whose frequency in the population is unclear.
.
TIgGER is a computational method that significantly improves V(D)J
allele assignments by first determining the complete set of gene segments
carried by an individual (including novel alleles) from V(D)J-rearrange
sequences. TIgGER can then infer a subject’s genotype from these
sequences, and use this genotype to correct the initial V(D)J allele
assignments.
.
The application of TIgGER continues to identify a surprisingly high
frequency of novel alleles in humans, highlighting the critical need
for this approach. TIgGER, however, can and has been used with data
from other species.
.
Core Abilities:
* Detecting novel alleles
* Inferring a subject’s genotype
* Correcting preliminary allele calls
.
Required Input
* A table of sequences from a single individual, with columns containing
the following:
- V(D)J-rearranged nucleotide sequence (in IMGT-gapped format)
- Preliminary V allele calls
- Preliminary J allele calls
- Length of the junction region
* Germline Ig sequences in IMGT-gapped fasta format (e.g., as those
downloaded from IMGT/GENE-DB)
.
The former can be created through the use of IMGT/HighV-QUEST and
Change-O.
Description-md5: 7bedf1181b6cce84d2b1c1d9dac6be75