0.5.4

immunarch 0.5.4

We are 0.5.4 now!

1. Tracking clonotypes across time points

   • We updated Tracking clonotypes across time points tutorial
   • More tweaks and examples were shown
   • In Changing the colour palette section we shown how to change palette colors
   • In Changing the order of samples section we demonstrated how to control the order of samples in visualisations

2. Gene usage analysis

   • We updated gene segments tables with new segments for BosTaurus, MusMusculus and HomoSapiens with IMGT database. So gene usage function is up-to-date now.

3. Data input

   • Clonotype counting is fixed now

4. Single-cell analysis

   • We added a new function filter_barcodes for filtering by barcodes for single-cell data

5. Immunarch.com

   • We added Search field to the website to make docs more available for you

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feat(vignette): update information about outdated packages in the "installation troubleshooting" section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

0.4.3

immunarch 0.4.3

Features

• chore(upkeep): add new vignettes to the website
• feat(io): add a correct parsing for 10xGenomics data with splitting repertoires by chain type + metadata auto-update for such cases
• docs(vignette): add a vignette for kmer analysis
• docs(vignette): add a vignette for clonotype tracking
• docs(upkeep): update README to add a new method to install the package and make it more clear and focused on the installation process

Minor updates

• chore(upkeep): changelog link now leads to github
• fix(upkeep): fix indents in README
• fix(vignette): fix a bug with non-unique vignette names
• chore(upkeep): add links to the new vignettes to the README file
• docs(io): update docs for repLoad
• chore(upkeep): version bump

Bug fixes

• fix(vignette): minor fixes for vignettes: remove warnings, update info on the package installation

0.4.1

immunarch 0.4.1

Features

• feat(diversity): aded a column choice for repDiversity

Minor updates

• Continuous integration process improved. We are heading towards improvements in code and commit organization in the repository.
• Some parts were refactored: explore, inst, io, kmers, overlap, package, public-repertoire, shiny, spectratype, tests.
• Improved tests for: clonality, diversity, dynamics, explore, gene-usage, kmers, overlap, public-repertoire.
• Docs: general improvements, fixed typos.

Bug fixes

• fix(clonality): fix docs in repDiversity, prepare to CRAN check
• fix(diversity): fix docs in repDiversity, prepare to CRAN check
• fix(diversity): fix R check from repDiversity
• fix(gene-usage): add a comment for a future fix, make it work with data.tables properly
• fix(io): fix a bug when .compress=F doesn't work in repSave if .format = "immunarch"
• fix(package): fix CRAN NOTE about dtplyr
• fix(package): change version to 0.4.0.9000 and fix the description for the CRAN release
• fix(public-repertoire): fix .coding doesn't work
• fix(tests): fix clonality tests
• fix(tests): fix spectratyping tests
• fix(tests): fix overlap tests
• fix(tests): remove unnecessary print() from spectratype testing
• fix(vignette): fix spectratype in the vignette

0.4.0

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.

0.3.3

immunarch 0.3.3

Parser for ArcherDX.

Replace all "unresolved" genes in ImmunoSEQ parsed files with NAs.

Add an argument for the color palette to vis_heatmap2.

Make .grid=F by default in vis_hist for gene usage analysis.

Update a parser for MiXCR to make it work with the "targetSequences" column format.

Fix parsing functions to not remove strings after dots in filenames.

Update the coding function family to make it work with CDR3 amino acid sequences only.

Add a documentation to the coding function family.

Update the post-parsing processing subroutine to remove all characters except for amino acid alphabet, * and ~ for compatability with all immunarch's functions.

Update README.

0.3.2

Remove MonetDBLite because it got removed from CRAN causing all the installation issues.

Fix MiXCR parser.

0.3.1

update social

0.3.0

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