Make README more clear with the focus on installation.
Add a vignette for clonotype tracking.
Add a vignette for kmer analysis.
Kmers - analysis + plots, seqlogo / textlogo
pubRepStatistics function for computation of publicclonotypes across groups and repertoires.
vis_public_frequencies,vis_public_clonotypes,vis_upset for publicrepertoire visualisations.
Minor releases with bug fixes and minor improvements.
ThetrackClonotype function for tracking clonotypes.
Visualisations fortrackClonotype.
Speed up Morisita-Horn index computation for up to 3 times.
Add the incremental overlap functioninc_overlap,available fromrepOverlap.
Add the downsampling option to incremental overlaps.
Add visualisations for incvremental overlaps.
Remove theprop_sample function completely.
Move all downsampling, resampling and sampling procedures to therepSample function.
Add normalisation to rarafection.
Remove the .dup argument fromrepOverlap, all equalclonotypes are now always merged and their counts summed up.
Remove .quant fromrepOverlap, the column is nowautomatically detected.
Add an argument .add.layer tovis_hist to add anyadditional ggplot2 layers to the plots in the output grid.
Add grouping invis_hist if data is grouped and.grid is T.
Update MiXCR parser (yet again) to read MiXCR files from the May 2019release.
Add.target argument to visualisation of incrementaloverlaps.
Add.clones torepExplore.
Add more MiXCR file variants parsing.
repLoad returns sorted by “Clones” data frames now.
FixgeneUsage when the first two columns with geneusages were swapped.
FixrepExplore doesn’t work with a singlerepertoire.
Fixvis_heatmap doesn’t work withgeneUsageoutput.
Fix a bug in computation of Morisita-Horn index.
Fixvis_bar andvis_box doesn’t work withnumeric grouping variables.
FixrepOverlap failing when working on data tables withmorisita.
FixrepOverlap failing to work with data tables onpublic,overlap,jaccard andtversky.
FixrepLoad failing when parsing MiXCR files with zeroclonotypes.
Fix a bug in incorrect grouping in visualisations.
Fix a bug when clonal homeostasis and clonotype tracking don’t workproperly with filtered coding.
Fix D50, “top” and “clonal.prop” from repClonality returns wrongvalues when the input data frame is not sorted.
Remove the “wei” option fromgeneUsage becase it’suseless.
New dependencyggseqlogo for visualising of seq-logoplots.
Add.transpose tovis_heatmap.
repOverlap default .col value is “aa” for comfortableusage.
Remove “fill” aesthetics warnings fromvis_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 theCRAN release.
Remove short function names.
Parser for ArcherDX.
Update a parser for MiXCR to make it work with the “targetSequences”column format.
Update the coding function family to make it work with CDR3 aminoacid sequences only.
Replace all “unresolved” genes in ImmunoSEQ parsed files withNAs.
Add an argument for the color palette tovis_heatmap2.
Make.grid=F by default invis_hist forgene usage analysis.
Fix parsing functions to not remove strings after dots infilenames.
Update the post-parsing processing subroutine to remove allcharacters except for amino acid alphabet,* and~ for compatability with allimmunarch’sfunctions.
Add a documentation to the coding function family.
Update README.
Remove MonetDBLite from dependencies because it got removed fromCRAN.
Boxplots and barplots are now support statistical tests via the.test argument.
Add parsers for old VDJtools formats.
Update docs and vignettes with statistical testsinformation.
Add a note for list names to vignettes.
Documentation for clustering.
Documentation for dimension reduction.
Minor fix forrepOverlap documentation.
Fix a grouping bug in visualisations.
Fix statistical tests fromggpubr.
Fix forgeneUsage with.type="family".
fixVis now supports the following legends: size,shape, color, fill, linetype.
fixVis can plot figures to R console / RStudio“Plots” tab.
fixVis now supports the number of columns inlegends.
Support for the AIRR file format.
Experimental support for the 10xGenomics format.
Save and loadimmunarch format viarepSave andrepLoad.
Save and load VDJtools format viarepSave andrepLoad.
.a and.b didn’t passed to Tverskyindex.
fixVis - fix a bug when users apply X/Y settings tothe other axis.