Package: ogrdbstats 0.5.3
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:
ogrdbstats_0.5.3.tar.gz
ogrdbstats_0.5.3.zip(r-4.5)ogrdbstats_0.5.3.zip(r-4.4)ogrdbstats_0.5.3.zip(r-4.3)
ogrdbstats_0.5.3.tgz(r-4.5-any)ogrdbstats_0.5.3.tgz(r-4.4-any)ogrdbstats_0.5.3.tgz(r-4.3-any)
ogrdbstats_0.5.3.tar.gz(r-4.5-noble)ogrdbstats_0.5.3.tar.gz(r-4.4-noble)
ogrdbstats_0.5.3.tgz(r-4.4-emscripten)ogrdbstats_0.5.3.tgz(r-4.3-emscripten)
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
- example_rep - Example repertoire data
Last updated 4 days agofrom:4e544af5e8. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 16 2025 |
| R-4.5-win | OK | Feb 16 2025 |
| R-4.5-mac | OK | Feb 16 2025 |
| R-4.5-linux | OK | Feb 16 2025 |
| R-4.4-win | OK | Feb 16 2025 |
| R-4.4-mac | OK | Feb 16 2025 |
| R-4.3-win | OK | Feb 16 2025 |
| R-4.3-mac | OK | Feb 16 2025 |
Exports:generate_ogrdb_reportgenotype_statistics_cmdmake_barplot_grobsmake_haplo_grobsmake_novel_base_grobsread_input_fileswrite_genotype_filewrite_plot_file
Dependencies:abindade4airralakazamapeargparseraskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsbookdownbslibcachemcirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesGetoptLongggplot2GlobalOptionsgluegridExtragtablegtoolshighrhmshtmltoolshttrigraphIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpixmappkgconfigpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloreadrRhtslibrjsonrlangrmarkdownRsamtoolsS4ArraysS4VectorssassscalessegmentedseqinrshapesnowspSparseArraystringdiststringistringrSummarizedExperimentsystibbletidyrtidyselecttiggertinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXVectoryaml
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 |
