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10x format in repLoad(): added C genes support
Support for vdjtools format with "freq" header instead of "frequency"
Bugfix for filter: exclude must not remove everything when string is not matching
Germline formulas fixes
Fixed "missing value" error in repDiversity
Deprecated .format argument removed from repLoad
Various bugfixes in code and documentation

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BCR pipeline implementation: seqDist(), seqCluster(), repGermline(), repAlignLineage() and repClonalFamily() functions
New example data for BCR: small version can be loaded with data(bcrdata), large version is available on this page in Assets
MiXCR parser in repLoad() now loads C genes, CDR3 begin/end coordinates and number of insertions/deletions in V and J genes
Added parameter for vis_heatmap(): .axis.text.size
Various bugfixes in code and documentation

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Add MiXCR v2 support; repLoad() now returns the index of the currently parsed file in the output
Add CDR1-2-3/FR1-2-3-4 column names to the extended immunarch format
Fix a bug in public repertoires with the data table output
Hadley's pull request, remove a deprecated function
Hadley's pull request, use a proper function for setting up a data.table
Fix a bug with the wrong order to Mean and Q1 columns in rarefaction
MiXCR parser doesn't sort genes by the alphabetical order anymore
Add parsers for CATT, RTCR, Imseq and Vidjil formats
Add columns for CDR1 and CDR2 to MiXCR parser
Support for TRUST4 format in repLoad
Fix for .which_recomb_type failed on empty input files
Fix for .signif.digits bug in vis()
Fix for error that parser failed on files without data
Add repFilter() function
Add automatic docker builds for Immunomind's Dockerhub
Support for loading AIRR files in .csv format
Various fixes for data loading
Small fixes and cleanups
Update documentation and tutorials

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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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immunarch is 0.6.4 now!

News

  1. Updated website with better documentation.
  2. We embedded email registration on the front page. Get in touch, we are ready to it!
  3. The package is now could be installed via devtools::install_github("immunomind/immunarch").

Fixed Issues

Comprehensive issue list since 0.5.5.

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immunarch 0.5.5

We are 0.5.5 now! This is a minor release.

  1. Data input

    • We fixed incorrect parsing of MiXCR for files with ","
  2. Gene usage analysis

    • We fixed gene usage function. An option to handle ambiguous data .ambig="maj" is now working correctly on non-IMGT genes.
    • We fixed gene usage function bug when applied to a list of a single element didn't work.
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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
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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.

--

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 鈥榝coalesce鈥 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

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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
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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