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r-cran-tigger package

r-cran-tigger 1.1.0-1 source package in Ubuntu

Changelog

r-cran-tigger (1.1.0-1) unstable; urgency=medium

  * Team upload.
  * Disable reprotest
  * Standards-Version: 4.6.2 (routine-update)
  * dh-update-R to update Build-Depends (routine-update)

 -- Andreas Tille <email address hidden>  Fri, 27 Oct 2023 15:00:38 +0200

Upload details

Uploaded by:
Debian R Packages Maintainers
Uploaded to:
Sid
Original maintainer:
Debian R Packages Maintainers
Architectures:
all
Section:
misc
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section
Oracular release universe misc
Noble release universe misc

Builds

Noble: [FULLYBUILT] amd64

Downloads

File Size SHA-256 Checksum
r-cran-tigger_1.1.0-1.dsc 2.2 KiB 24208afe64c6b7d8ceb764557c097677169fd9a638bb877cb50edaa148124182
r-cran-tigger_1.1.0.orig.tar.gz 2.7 MiB caed8aaaeb4bbeecd49f5980b678044cad09939bb1827d40efc44742fd7b050b
r-cran-tigger_1.1.0-1.debian.tar.xz 7.7 KiB 4b6abb7dbe5338c327d7123abcfb35ceb503449b7db0819885cd95671b50d447

Available diffs

No changes file available.

Binary packages built by this source

r-cran-tigger: 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.