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Source: r-cran-tigger
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Uploaders: Steffen Moeller <moeller@debian.org>
Section: gnu-r
Testsuite: autopkgtest-pkg-r
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-r,
r-base-dev,
r-cran-ggplot2 (>= 3.4.0),
r-cran-alakazam (>= 1.3.0),
r-cran-dplyr,
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
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-cran-tigger
Vcs-Git: https://salsa.debian.org/r-pkg-team/r-cran-tigger.git
Homepage: https://cran.r-project.org/package=tigger
Rules-Requires-Root: no
Package: r-cran-tigger
Architecture: all
Depends: ${R:Depends},
${misc:Depends}
Recommends: ${R:Recommends}
Suggests: ${R:Suggests}
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.
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