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immunomind/immunarch: 0.6.5: Basic single-cell support

Vadim Nazarov; immunarch.bot; Eugene Rumynskiy

fix(vignette): fix incorrect CRAN links in the Introduction vignette refactor(data): make the data smaller in order to follow the CRAN guidelines refactor(web): fix paths to the moved Basic Analysis vignette refactor(vignette): remove the Basic Analysis vignette from the CRAN pacakge refactor(vignette): add the tracking visualisation to the single-cell vignette fix(vignette): remove https because it fails on CRAN checks feat(upkeep): update README & NAMESPACE to reflect the single-cell support and also shorten the documentation for readability fix(io): fix imports fix(single-cell): fix the missing barcode column feat(data): add the "scdata" dataset with paired chain data and barcodes docs(io): update docs for repLoad / repSave to reflect single-cell support docs(single-cell): add docs for select_barcodes feat(vignette): finish the single-cell vignette feat(vignette): add a draft for the single-cell vignette refactor(upkeep): add "single-cell" and "data" commit scopes feat(io): add a paired chain parsing support for 10X feat(data): add new test files for single-cell docs(single-cell): add docs for single-cell functions docs(upkeep): update the docs for bulk data feat(upkeep): add the single-cell example data feat(web): add the single-cell vignette feat(single-cell): add a support for filtering and selecting clonotypes by barcodes and the Seurat::Idents() output refactor(io): remove raw_contig and raw_clonotype columns from 10X data to reduce the memory print feat(upkeep): add a new environment for additional immunarch columns fix(io): update the repLoad docs feat(io): add the ".coding" argument to filter out non-coding sequences (ON by default) chore(vignette): add badges for the optimisation of looking for downloads statistics chore(tools): move filter_barcodes() to singlecell.R and rename it to select_barcodes() chore(db): rename search.R with annotation.R chore(pub-rep): rename shared.R to public.R chore(tools): rename processing.R to sampling.R chore(data): move the description of "immdata" to data_docs.R chore(tools): move data filtering & manipulation functions to the preprocessing.R file refactor(io) / refactor(vignette): focus on the automatic detection of file formats refactor(upkeep): change authors to contributors feat(io): add "report" and "vdjca" files to the ignore list refactor(io): put a warning when .format is provided, and update repLoad documentation skip this comment in NEWS: add IO_REFACTOR label to where I experimented with data.table-based input reading. Initial benchmarks shows x2 acceleration in data loading speed fix(vis): fix a bug #65 in plotting repClonality with .col="nt" (PR #66 from Rushil) refactor(upkeep): add pull requests names to the contribution guide fix(vis): fix a bug in clonality visualisations #65 (PR #66) refactor(upkeep): update the contribution guide refactor(vignette): remove treemap and replace gridExtra with patchwork refactor(vis): remove treemap and replace gridExtra with patchwork fix(vignette): replace "develop" with "dev" refactor(tools): add_class() now adds the class to the beginning of the class attributes in order to comply with the R class system feat(vignette): cosmetic changes to the README feat(upkeep): add the pkgdown folder to the ignore feat(upkeep): remove "Home" and "News", add a link to the covid-19 repo feat(vignette): make the README more succinct, add a quick start section and the visitors badge refactor(upkeep): minor changes in text feat(upkeep): add the tag for the website refactor(io): refactor warning messages to make them more correct & add "na.rm = TRUE" to eliminates NAs when computing new Proportion columns

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