Paketti: r-cran-tigger (0.3.1-1)

[ 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.

Muut pakettiin r-cran-tigger liittyvät paketit

• dep: r-api-3.5

  näennäispaketti, jonka toteuttaa r-base-core

• dep: r-base-core (>= 3.5.1-1)

  GNU R core of statistical computation and graphics system

• dep: r-cran-alakazam (>= 0.2.11)

  Immunoglobulin Clonal Lineage and Diversity Analysis

• dep: r-cran-doparallel

  GNU R foreach parallel adaptor for the parallel package

• dep: r-cran-dplyr (>= 0.7.0)

  GNU R grammar of data manipulation

• dep: r-cran-foreach

  GNU R foreach looping support

• dep: r-cran-ggplot2 (>= 2.0.0)

  implementation of the Grammar of Graphics

• dep: r-cran-gridextra

  GNU R package with extensions for the grid package

• dep: r-cran-gtools

  GNU R package with R programming tools by Greg Warnes et al

• dep: r-cran-iterators

  GNU R iterator support for vectors, lists and other containers

• dep: r-cran-lazyeval

  GNU R lazy (non-standard) evaluation

• dep: r-cran-rlang

  Functions for Base Types and Core R and 'Tidyverse' Features

• dep: r-cran-shazam (>= 0.1.10)

  Immunoglobulin Somatic Hypermutation Analysis

• dep: r-cran-stringi

  GNU R character string processing facilities

• dep: r-cran-tidyr

  GNU R package to easily tidy data

• sug: r-cran-knitr

  GNU R package for dynamic report generation using Literate Programming

• sug: r-cran-testthat

  GNU R testsuite

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