deb_control_files:
- control
- md5sums
deb_fields:
Architecture: all
Depends: r-api-4.0, r-cran-ggplot2 (>= 3.4.0), r-cran-alakazam (>= 1.3.0), r-cran-dplyr
(>= 1.0.0), 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
(>= 1.1.0)
Description: "Infers new Immunoglobulin alleles from Rep-Seq Data\n Summary: Infers\
\ the V genotype of an individual from immunoglobulin (Ig)\n repertoire-sequencing\
\ (Rep-Seq) data, including detection of any novel\n alleles. This information\
\ is then used to correct existing V allele calls\n from among the sample sequences.\n\
\ .\n High-throughput sequencing of B cell immunoglobulin receptors is\n providing\
\ unprecedented insight into adaptive immunity. A key step in\n analyzing these\
\ data involves assignment of the germline V, D and J gene\n segment alleles that\
\ comprise each immunoglobulin sequence by matching\n them against a database\
\ of known V(D)J alleles. However, this process\n will fail for sequences that\
\ utilize previously undetected alleles,\n whose frequency in the population is\
\ unclear.\n .\n TIgGER is a computational method that significantly improves\
\ V(D)J\n allele assignments by first determining the complete set of gene segments\n\
\ carried by an individual (including novel alleles) from V(D)J-rearrange\n sequences.\
\ TIgGER can then infer a subject\u2019s genotype from these\n sequences, and\
\ use this genotype to correct the initial V(D)J allele\n assignments.\n .\n The\
\ application of TIgGER continues to identify a surprisingly high\n frequency\
\ of novel alleles in humans, highlighting the critical need\n for this approach.\
\ TIgGER, however, can and has been used with data\n from other species.\n .\n\
\ Core Abilities:\n * Detecting novel alleles\n * Inferring a subject\u2019\
s genotype\n * Correcting preliminary allele calls\n .\n Required Input\n *\
\ A table of sequences from a single individual, with columns containing\n \
\ the following:\n - V(D)J-rearranged nucleotide sequence (in IMGT-gapped\
\ format)\n - Preliminary V allele calls\n - Preliminary J allele calls\n\
\ - Length of the junction region\n * Germline Ig sequences in IMGT-gapped\
\ fasta format (e.g., as those\n downloaded from IMGT/GENE-DB)\n .\n The former\
\ can be created through the use of IMGT/HighV-QUEST and\n Change-O."
Homepage: https://cran.r-project.org/package=tigger
Installed-Size: '4159'
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Package: r-cran-tigger
Priority: optional
Section: gnu-r
Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat
Version: 1.1.0-1
srcpkg_name: r-cran-tigger
srcpkg_version: 1.1.0-1