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Package: r-cran-alakazam (0.3.0-1build1)

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.

Other Packages Related to r-cran-alakazam

  • depends
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  • dep: libc6 (>= 2.14) [amd64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
    dep: libc6 (>= 2.4) [armhf]
  • dep: libgcc-s1 (>= 3.0) [amd64]
    GCC support library
    dep: libgcc-s1 (>= 3.5) [armhf]
  • dep: libstdc++6 (>= 5.2)
    GNU Standard C++ Library v3
  • dep: r-api-3.5
    virtual package provided by r-base-core
  • dep: r-base-core (>= 3.6.2.20200221-1build1)
    GNU R core of statistical computation and graphics system
  • dep: r-cran-ape
    GNU R package for Analyses of Phylogenetics and Evolution
  • dep: r-cran-dplyr (>= 0.8.1)
    GNU R grammar of data manipulation
  • dep: r-cran-ggplot2 (>= 2.0.0)
    implementation of the Grammar of Graphics
  • dep: r-cran-igraph (>= 1.0.0)
    GNU R network analysis and visualization
  • dep: r-cran-lazyeval
    GNU R lazy (non-standard) evaluation
  • dep: r-cran-matrix
    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
    GNU R package to easily tidy data

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Architecture Package Size Installed Size Files
amd64 1,699.9 kB2042 kB [list of files]
armhf 1,695.8 kB2001 kB [list of files]