r-cran-tigger 1.0.1-1 source package in Ubuntu
Changelog
r-cran-tigger (1.0.1-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) * dh-update-R to update Build-Depends (routine-update) * Set upstream metadata fields: Repository. -- Andreas Tille <email address hidden> Mon, 26 Sep 2022 15:05:32 +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 | Published | Component | Section | |
|---|---|---|---|---|
| Mantic | release | universe | misc | |
| Lunar | release | universe | misc |
Downloads
| File | Size | SHA-256 Checksum |
|---|---|---|
| r-cran-tigger_1.0.1-1.dsc | 2.2 KiB | cfc37a4cce2efc676748d156c7643ed226dcbfe480e2b9a758a394adfb7139d5 |
| r-cran-tigger_1.0.1.orig.tar.gz | 2.7 MiB | d47f90836e024c158dafdca55aa15a0b1b4d363e37bc6693324512ddc4e3118c |
| r-cran-tigger_1.0.1-1.debian.tar.xz | 7.5 KiB | edbe0e6a9ad4bd8fc3d88a8608533d6aa56826b28e5839277c66225fba395564 |
Available diffs
- diff from 1.0.0-1 to 1.0.1-1 (11.2 KiB)
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.
