套件：r-cran-alakazam（1.3.0-1） [debports]
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.
其他與 r-cran-alakazam 有關的套件
|
|
|
|
-
- dep: libc6.1 (>= 2.11)
- GNU C 函式庫：共用函式庫
同時作為一個虛擬套件由這些套件填實： libc6.1-udeb
-
- dep: libgcc-s1 (>= 3.4)
- GCC 支援函式庫
-
- dep: libstdc++6 (>= 13.1)
- GNU Standard C++ Library v3
-
- dep: r-api-4.0
- 本虛擬套件由這些套件填實： 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