Pakiet: r-cran-alakazam (1.3.0-1)

[ Pakiet źródłowy: r-cran-alakazam  ]

Immunoglobulin Clonal Lineage and Diversity Analysis

Alakazam is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides a set of tools to investigate lymphocyte receptor clonal lineages, diversity, gene usage, and other repertoire level properties, with a focus on high-throughput immunoglobulin (Ig) sequencing.

Alakazam serves five main purposes:

 * Providing core functionality for other R packages in the Immcantation
   framework. This includes common tasks such as file I/O, basic DNA
   sequence manipulation, and interacting with V(D)J segment and gene
   annotations.
 * Providing an R interface for interacting with the output of the
   pRESTO and Change-O tool suites.
 * Performing lineage reconstruction on clonal populations of Ig
   sequences and analyzing the topology of the resultant lineage trees.
 * Performing clonal abundance and diversity analysis on lymphocyte
   repertoires.
 * Performing physicochemical property analyses of lymphocyte receptor
   sequences.

Inne pakiety związane z r-cran-alakazam

• dep: libc6 (>= 2.14)

  Biblioteka GNU C: biblioteki współdzielone
  również pakiet wirtualny udostępniany przez libc6-udeb

• dep: libgcc-s1 (>= 3.0)

  Biblioteka wspomagająca GCC

• dep: libstdc++6 (>= 13.1)

  Standardowa biblioteka GNU C++, wersja 3

• dep: r-api-4.0

  pakiet wirtualny udostępniany przez r-base-core

• dep: r-bioc-biostrings (>= 2.56.0)

  GNU R string objects representing biological sequences

• dep: r-bioc-genomicalignments (>= 1.24.0)

  BioConductor representation and manipulation of short genomic alignments

• dep: r-bioc-iranges (>= 2.22.2)

  GNU R low-level containers for storing sets of integer ranges

• dep: r-cran-airr (>= 1.4.1)

  GNU R AIRR data representation reference library

• dep: r-cran-ape

  GNU R package for Analyses of Phylogenetics and Evolution

• dep: r-cran-dplyr (>= 1.0)

  GNU R grammar of data manipulation

• dep: r-cran-ggplot2 (>= 3.4.0)

  implementation of the Grammar of Graphics

• dep: r-cran-igraph (>= 1.5.0)

  GNU R network analysis and visualization

• dep: r-cran-matrix (>= 1.3-0)

  GNU R package of classes for dense and sparse matrices

• dep: r-cran-progress

  GNU R terminal progress bars

• dep: r-cran-rcpp (>= 0.12.12)

  GNU R package for Seamless R and C++ Integration

• dep: r-cran-readr

  GNU R package to read rectangular text data

• dep: r-cran-rlang

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

• dep: r-cran-scales

  Scale functions for visualization

• dep: r-cran-seqinr

  GNU R biological sequences retrieval and analysis

• dep: r-cran-stringi

  GNU R character string processing facilities

• dep: r-cran-tibble

  GNU R Simple Data Frames

• dep: r-cran-tidyr (>= 1.0)

  GNU R package to easily tidy data

• sug: r-cran-knitr

  GNU R package for dynamic report generation using Literate Programming

• sug: r-cran-rmarkdown

  convert R markdown documents into a variety of formats

• sug: r-cran-testthat

  GNU R testsuite

Pobieranie r-cran-alakazam

Pobierz dla wszystkich dostępnych architektur

Architektura	Rozmiar pakietu	Rozmiar po instalacji	Pliki
amd64	2 362,0 KiB	2 845,0 KiB	[lista plików]