Title: immunarch: An R Package for Painless Analysis of Large-Scale Immune Repertoire Data

Type Software ImmunoMind Team (2019): immunarch: An R Package for Painless Analysis of Large-Scale Immune Repertoire Data. Zenodo. Software. https://zenodo.org/record/3367201

Author: ImmunoMind Team ;

Links

• Item record in Zenodo
• Digital object URL

Summary

immunarch 0.4.0 Features

The trackClonotype function for tracking clonotypes.

Visualisations for trackClonotype.

Speed up Morisita-Horn index computation for up to 3 times.

Add the incremental overlap function inc_overlap, available from repOverlap.

Add the downsampling option to incremental overlaps.

Add visualisations for incvremental overlaps.

Remove the prop_sample function completely.

Move all downsampling, resampling and sampling procedures to the repSample function.

Add normalisation to rarafection.

Remove the .dup argument from repOverlap, all equal clonotypes are now always merged and their counts summed up.

Remove .quant from repOverlap, the column is now automatically detected.

Add an argument .add.layer to vis_hist to add any additional ggplot2 layers to the plots in the output grid.

Add grouping in vis_hist if data is grouped and .grid is T.

Update MiXCR parser (yet again) to read MiXCR files from the May 2019 release.

Add .target argument to visualisation of incremental overlaps.

Add .clones to repExplore.

Add more MiXCR file variants parsing.

repLoad returns sorted by "Clones" data frames now.

Bug fixes

Fix geneUsage when the first two columns with gene usages were swapped.

Fix repExplore doesn't work with a single repertoire.

Fix vis_heatmap doesn't work with geneUsage output.

Fix a bug in computation of Morisita-Horn index.

Fix vis_bar and vis_box doesn't work with numeric grouping variables.

Fix repOverlap failing when working on data tables with morisita.

Fix repOverlap failing to work with data tables on public, overlap, jaccard and tversky.

Fix repLoad failing when parsing MiXCR files with zero clonotypes.

Fix a bug in incorrect grouping in visualisations.

Fix a bug when clonal homeostasis and clonotype tracking don't work properly with filtered coding.

Fix D50, "top" and "clonal.prop" from repClonality returns wrong values when the input data frame is not sorted.

Minor updates

Remove the "wei" option from geneUsage becase it's useless.

New dependency ggseqlogo for visualising of seq-logo plots.

Add .transpose to vis_heatmap.

repOverlap default .col value is "aa" for comfortable usage.

Remove "fill" aesthetics warnings from vis_heatmap.

Remove warnings "In parse_fun(.path[i]) : NAs introduced by coercion" when parsing MiXCR files.

A lot or minor fixing and documentation improving to prepare for the CRAN release.

Remove short function names.

More information

• DOI: 10.5281/zenodo.3367201

Dates

• Publication date: 2019
• Issued: August 13, 2019

Rights

• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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