r-cran-tigger 0.3.1-1 source package in Ubuntu


r-cran-tigger (0.3.1-1) unstable; urgency=medium

  * Team upload.
  * New upstream version

 -- Andreas Tille <email address hidden>  Mon, 22 Oct 2018 11:39:15 +0200

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Uploaded by:
Debian R Packages Maintainers on 2018-10-22
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Original maintainer:
Debian R Packages Maintainers
Medium Urgency

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Series Pocket Published Component Section
Disco release on 2018-11-10 universe misc


Disco: [FULLYBUILT] amd64


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r-cran-tigger_0.3.1-1.dsc 2.2 KiB 9274ef92f054f81cd22af17ccf6bf605751161ef93ecc85205c84086e7defb13
r-cran-tigger_0.3.1.orig.tar.gz 1.5 MiB 2dc221be0a01a608bb9b0cd5e0cd44e257e14f7add46cd97fab729620e55c8ab
r-cran-tigger_0.3.1-1.debian.tar.xz 7.2 KiB c3ed20cfc1170aefa08a957a85b099413f8daa4cc814b3817b3eaba0b61c050c

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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
 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