0.6.5: Basic single-cell support

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