Source: r-cran-alakazam Maintainer: Debian R Packages Maintainers Uploaders: Steffen Moeller Section: gnu-r Testsuite: autopkgtest-pkg-r Priority: optional Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-cran-ggplot2 (>= 3.4.0), r-cran-airr (>= 1.4.1), r-cran-ape, r-cran-dplyr, r-cran-igraph (>= 1.5.0), r-cran-matrix, r-cran-progress, r-cran-rcpp, r-cran-readr, r-cran-rlang, r-cran-scales, r-cran-seqinr, r-cran-stringi, r-cran-tibble, r-cran-tidyr, r-bioc-biostrings (>= 2.72.1), r-bioc-genomicalignments (>= 1.40.0), r-bioc-iranges (>= 2.38.1) Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-cran-alakazam Vcs-Git: https://salsa.debian.org/r-pkg-team/r-cran-alakazam.git Homepage: https://cran.r-project.org/package=alakazam Rules-Requires-Root: no Package: r-cran-alakazam Architecture: any Depends: ${R:Depends}, ${shlibs:Depends}, ${misc:Depends}, r-bioc-biostrings (>= 2.72.1), r-bioc-genomicalignments (>= 1.40.0), r-bioc-iranges (>= 2.38.1) Recommends: ${R:Recommends} Suggests: ${R:Suggests} Description: 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.