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Package: r-cran-alakazam (1.2.0-1)

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
  • recommends
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  • dep: libc6 (>= 2.14) [amd64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
    dep: libc6 (>= 2.17) [arm64, ppc64el]
    dep: libc6 (>= 2.4) [armhf]
  • dep: libgcc-s1 (>= 3.3.1) [not armhf]
    GCC support library
    dep: libgcc-s1 (>= 3.5) [armhf]
  • dep: libstdc++6 (>= 5.2) [armhf]
    GNU Standard C++ Library v3
    dep: libstdc++6 (>= 9) [not armhf]
  • dep: r-api-4.0
    virtual package provided by r-base-core
  • dep: r-base-core (>= 4.1.2-1)
    GNU R core of statistical computation and graphics system
  • 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 (>= 1.3)
    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 (>= 3.3.4)
    implementation of the Grammar of Graphics
  • dep: r-cran-igraph (>= 1.0)
    GNU R network analysis and visualization
  • 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 (>= 1.0)
    GNU R package to easily tidy data

Download r-cran-alakazam

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 2,328.9 kB2774 kB [list of files]
arm64 2,326.5 kB2761 kB [list of files]
armhf 2,333.7 kB2753 kB [list of files]
ppc64el 2,333.5 kB2805 kB [list of files]