Package: ogrdbstats 0.5.1

William Lees

ogrdbstats: Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics

Multiple tools are now available for inferring the personalised germ line set from an adaptive immune receptor repertoire. Output from these tools is converted to a single format and supplemented with rich data such as usage and characterisation of 'novel' germ line alleles. This data can be particularly useful when considering the validity of novel inferences. Use of the analysis provided is described in <doi:10.3389/fimmu.2019.00435>.

Authors:William Lees [aut, cre]

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ogrdbstats.pdf |ogrdbstats.html✨
ogrdbstats/json (API)
NEWS

# Install 'ogrdbstats' in R:

install.packages('ogrdbstats', repos = c('https://airr-community.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/airr-community/ogrdbstats/issues

Datasets:

example_rep - Example repertoire data

On CRAN:

8 exports 1 stars 0.84 score 133 dependencies 8 scripts 266 downloads

Last updated 9 months agofrom:167edff985. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 15 2024
R-4.5-win	OK	Sep 15 2024
R-4.5-linux	OK	Sep 15 2024
R-4.4-win	OK	Sep 15 2024
R-4.4-mac	OK	Sep 15 2024
R-4.3-win	OK	Sep 15 2024
R-4.3-mac	OK	Sep 15 2024

Exports:generate_ogrdb_report genotype_statistics_cmd make_barplot_grobs make_haplo_grobs make_novel_base_grobs read_input_files write_genotype_file write_plot_file

Dependencies:abind ade4 airr alakazam ape argparser askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops bookdown bslib cachem circlize cli clipr clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl data.table DelayedArray digest doParallel dplyr evaluate fansi farver fastmap fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges GetoptLong ggplot2 GlobalOptions glue gridExtra gtable gtools highr hms htmltools httr igraph IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pixmap pkgconfig png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo readr Rhtslib rjson rlang rmarkdown Rsamtools S4Arrays S4Vectors sass scales segmented seqinr shape snow sp SparseArray stringdist stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tigger tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XVector yaml zlibbioc

Using ogrdbstats

William Lees

Rendered fromusing_ogrdbstats.Rmdusingknitr::rmarkdownon Sep 15 2024.

Last update: 2023-03-08
Started: 2019-10-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example repertoire data	example_rep
Generate OGRDB reports from specified files.	generate_ogrdb_report
Collect parameters from the command line and use them to create a report and CSV file	genotype_statistics_cmd
Create a barplot for each allele, showing number of reads distributed by mutation count	make_barplot_grobs
Create haplotyping plots	make_haplo_grobs
Create plots showing base usage at selected locations in sequences based on novel alleles	make_novel_base_grobs
Read input files into memory	read_input_files
Write the genotype file required by OGRDB	write_genotype_file
Create the OGRDB style plot file	write_plot_file