0.5.2

immunarch 0.5.2

We are 0.5.2 now!

The changes are:

1. We organized tutorials in more convenient way, so now there are several sections:

   • First steps
   • Explore and compare repertoires
   • Preparing to publication
   • Advanced methods

2. It is now possible to find antigen-specific receptors using your data and external databases like VDJDB, McPAS-TCR, TBAdb from PIRD.

   • We added new functions:dbAnnotate(...), dbLoad(...) check Reference for details
   • And created vignette to show how to use them - Annotate clonotypes using immune receptor databases

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List of commits

Features:
feat(upkeep): verison bump
feat(vignette): add installation instructions for CRAN
feat(db): add dbLoad for loading databases
feat(db): add a database annotation basic functionality
docs(db): add docs for dbAnnotate and dbLoad
docs(vignette): add a full vignette for database annotation
docs(vignette): make quick start more clear
docs(vignette): update README with new installation troubleshooting instructions
feat(upkeep): add a new installation troubleshooting point for mac users
feat(vignette): update information about outdated packages in the "installation troubleshooting" section
feat(clonality): add "other" clonotypes to the rare clonotypes computation to make sure all percentage summed up to 100
feat(io): add a support for filtered contig files from 10xGenomics
feat(upkeep): add readxl to dependencies

Fixes:
fix(chore): fix a path to the base Docker container
fix(clonality): add a compatability layer with dtplyr v1.0.0
fix(db): fix CRAN warnings: doi and database paths
fix(db): fix dbLoad don't load the "Epitope species" column for vdjdb search tables
fix(db): fix NOTES after CRAN check; add new checks for common errors
fix(diversity): add a compatability layer with dtplyr v1.0.0
fix(explore): compatability with dtplyr v1.0.0
fix(geneusage): compatability with dtplyr v1.0.0
fix(io): fix errors in reading metadata; make the parser more verbose; re-write it to process data step-by-step
fix(io): fix warnings !is.na(.add)
fix(overlap): add a compatability layer with dtplyr v1.0.0
fix(public-repertoire): compatability with dtplyr v1.0.0
fix(tools): compatability with dtplyr v1.0.0
fix(tools): fix group names creation for plots
fix(tools): remove quant_column_choise from export
fix(upkeep): add melt.data.table because otherwise vis.immune_dynamics breaks
fix(upkeep): data.table 1.12.6 is required now because of the "Error: object ‘fcoalesce’ is not exported by 'namespace:data.table'" bug
fix(upkeep): fix db files for the db vignette
fix(upkeep): fix NAMESPACE with dtplyr v1.0.0
fix(upkeep): update authors
fix(upkeep): version bump and LazyData: true
fix(upkeep): version bump, add V and add a detailed descriptions about the package for the CRAN release
fix(vignette): clearly state that we take IMGT genes
fix(vignette): fix CRAN warnings: bad URLs
fix(vignette): fix CRAN warnings: wrong URLs
fix(vignette): fix English, move advanced filtering to the end of the vignette
fix(vignette): fix file paths in the db vignette
fix(vignette): fix indentation in the "get started" vignette
fix(vignette): supress warning
fix(vis): fix data.table bug
refactor(clonality): replace "tail" with "rare" in docs and plots
refactor(clonality): replace "tail" with "rare" mode of execution for better understanding
refactor(db): fix warnings in readr_*
refactor(docs): update Roxygen to v7
refactor(explore): update docs with more clear information on the "count" mode, add checks for additional mode names since people tend to mistype
refactor(io): fix warnings in readr:read_*
refactor(upkeep): add sections to the "Tutorials" section
refactor(upkeep): few minor changes to make the package description more clear
refactor(upkeep): move installation troubleshooting to the get started
refactor(upkeep): put precise versions to difficult-to-update packages
refactor(upkeep): remove link to the list of tutorials
refactor(vignette): change a link to the list of tutorials
refactor(vignette): move some vignettes outside the package to reduce the package's size
refactor(vignette): replace "tail" with "rare"
refactor(vis): use the "Spectral" palette more often purely for aesthetic purposes