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r-cran-tigger_1.0.1-1_all.deb
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مشاهده بیشتر
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مشاهده بیشترتوضیحات
Infers new Immunoglobulin alleles from Rep-Seq Data
| ویژگی | مقدار |
|---|---|
| سیستم عامل | Linux |
| توزیع | Debian Bookworm-12 |
| مخزن | Debian main all |
| نام بسته | r-cran-tigger |
| نام فایل بسته | r-cran-tigger_1.0.1-1_all.deb |
| نسخه بسته | 1.0.1 |
| انتشار بسته | 1 |
| معماری بسته | all |
| نگهدارنده | Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net> |
| تاریخ ساخت | - |
| هاست سازنده | - |
| نوع بسته | .deb |
| آدرس صفحه اصلی | https://cran.r-project.org/package=tigger |
| مجوز | - |
| حجم دانلود | 4096736 |
| حجم نصب | 4156 |
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.
نیازمندی
| مقدار | نام |
|---|---|
| >= 4.2.1-2 | r-base-core |
| - | r-api-4.0 |
| >= 3.2.0 | r-cran-ggplot2 |
| >= 1.1.0.999 | r-cran-alakazam |
| >= 0.8.1 | 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 |
| >= 0.1.0 | r-cran-tidyr |
نحوه نصب
نصب پکیج deb r-cran-tigger:
sudo apt-get install r-cran-tigger_1.0.1-1_all.deb
فایل ها
| مسیرها |
|---|
| ./usr/lib/R/site-library/tigger/CITATION |
| ./usr/lib/R/site-library/tigger/DESCRIPTION |
| ./usr/lib/R/site-library/tigger/INDEX |
| ./usr/lib/R/site-library/tigger/Meta/Rd.rds |
| ./usr/lib/R/site-library/tigger/Meta/data.rds |
| ./usr/lib/R/site-library/tigger/Meta/features.rds |
| ./usr/lib/R/site-library/tigger/Meta/hsearch.rds |
| ./usr/lib/R/site-library/tigger/Meta/links.rds |
| ./usr/lib/R/site-library/tigger/Meta/nsInfo.rds |
| ./usr/lib/R/site-library/tigger/Meta/package.rds |
| ./usr/lib/R/site-library/tigger/Meta/vignette.rds |
| ./usr/lib/R/site-library/tigger/NAMESPACE |
| ./usr/lib/R/site-library/tigger/NEWS.md |
| ./usr/lib/R/site-library/tigger/R/tigger |
| ./usr/lib/R/site-library/tigger/R/tigger.rdb |
| ./usr/lib/R/site-library/tigger/R/tigger.rdx |
| ./usr/lib/R/site-library/tigger/data/Rdata.rdb |
| ./usr/lib/R/site-library/tigger/data/Rdata.rds |
| ./usr/lib/R/site-library/tigger/data/Rdata.rdx |
| ./usr/lib/R/site-library/tigger/doc/Tigger-Vignette.R |
| ./usr/lib/R/site-library/tigger/doc/Tigger-Vignette.Rmd |
| ./usr/lib/R/site-library/tigger/doc/Tigger-Vignette.pdf |
| ./usr/lib/R/site-library/tigger/doc/index.html |
| ./usr/lib/R/site-library/tigger/help/AnIndex |
| ./usr/lib/R/site-library/tigger/help/aliases.rds |
| ./usr/lib/R/site-library/tigger/help/paths.rds |
| ./usr/lib/R/site-library/tigger/help/tigger.rdb |
| ./usr/lib/R/site-library/tigger/help/tigger.rdx |
| ./usr/lib/R/site-library/tigger/html/00Index.html |
| ./usr/lib/R/site-library/tigger/html/R.css |
| ./usr/share/doc/r-cran-tigger/changelog.Debian.gz |
| ./usr/share/doc/r-cran-tigger/copyright |