Package: r-cran-tigger
Version: 0.4.0-1
Architecture: all
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Original-Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 4159
Depends: r-base-core (>= 3.6.1-3), r-api-3.5, r-cran-ggplot2 (>= 3.1.1), r-cran-alakazam (>= 0.3.0), 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-shazam (>= 0.2.0), r-cran-stringi, r-cran-tidyr
Suggests: r-cran-knitr, r-cran-testthat
Section: gnu-r
Priority: optional
Homepage: https://cran.r-project.org/package=tigger
Description: 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.
