0.10.3.9002

What's Changed

• Deprecation warnings + function renaming + issue templates by @vadimnazarov in #450

Full Changelog: 0.10.3...0.10.3.9002

0.10.3

🧬 immunarch 0.10.3 — Release Notes

Highlights

• Single-cell support. Load single-cell AIRR data, pair chains, and link scRNA-seq or spatial metadata.
• Repertoire statistics. Key functions for gene usage, diversity, clonality, and publicness are implemented. More will come.
• Out-of-memory + rich annotation. Work with data bigger than RAM. Annotate receptors with any info (e.g., immunogenicity, gene expression, cluster). Powered by ImmunData from immundata package.
• Faster at scale. Major speed-ups for large cohorts and single-cell libraries thanks to DuckDB backend.
• More reproducible. Immutable data objects reduce side effects and make analyses repeatable.
• Easier to install. Multiple packages have been moved to "Suggests" and will be removed or moved to other packages later, making immunarch much more convenient to install.

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Migration notes (0.9 → 0.10)

• New data layer: ImmunData from immundata. Functions return new objects instead of mutating in place. This helps reproducibility and scaling.
• API changes: large “meta-functions” like repDiversity() split into small families such as airr_diversity_*. Use the shared prefixes and the family help pages (e.g., ?airr_diversity).
• Fewer heavy dependencies; faster install.
• Visualisation with vis() for the new API is still evolving. New vis() is focused on fast and convenient visualisations rather than publication-ready figures. For publication-ready plots, use ggplot2.

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Tutorials & How-tos

• Single-cell tutorial (end-to-end) — loading, QC, gene usage, clonality, diversity, public indices, annotation. [immunomind.github.io]
• Import old immunarch data — convert repLoad() to ImmunData with from_immunarch(...). ([immunomind.github.io]
• Read AIRR-C (bulk, single-cell), 10x Genomics (single-chain, paired-chain) — how-tos are available on the docs website. [immunomind.github.io]

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New / reworked analysis families (API reference)

These are the main v1.0-style families used in 0.10.3. Open the help in R (?family_name) or the API pages below.

airr_stats:            https://immunarch.com/reference/airr_stats.html
airr_public:           https://immunarch.com/reference/airr_public.html
airr_clonality:        https://immunarch.com/reference/airr_clonality.html
airr_diversity:        https://immunarch.com/reference/airr_diversity.html
annotate_clonality:    https://immunarch.com/reference/annotate_clonality.html

(These pages describe all functions in each family, e.g., airr_diversity_shannon(), airr_public_jaccard(), etc.)

Not all features from immunarch 0.9 are implemented in 0.10 yet. I'm working on it.

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Notes on immundata status

• immundata powers ImmunData and lets you analyse large datasets without loading everything in RAM. It supports bulk, single-cell, and spatial workflows. [immunomind.github.io]

Immunarch 0.9.1

What's Changed

• Dev by @vadimnazarov in #403

Full Changelog: 0.9.0...0.9.1

Immunarch 0.9.0

Added support for groups coloring on repClonalFamily() visualization with .vis_groups argument
Added support for MiXCR 4.1 input format
Added support for AIRR and 10x input formats for BCR pipeline
Fixed bug in repClonalFamily() with running phylip dnapars on Windows
Various small bugfixes

Immunarch 0.8.0

BCR pipeline now requires less columns in the input data: only nucleotide sequences of FR1-4 and CDR1-3 regions are needed
Bugfixes and performance improvements in BCR pipeline
Removed arguments .align_j_gene from repGermline() and .verbose_output from repAlignLineage() that are not needed anymore
seqDist() and seqCluster() now support auto-trimming of extra information from gene columns for proper cluster naming
New .trim_genes argument for seqDist() that allows to disable auto-trimming (useful if used columns are not ones with genes)
Improved clustering in seqCluster()
Removed some false warning that appeared on vis() calls

Immunarch 0.7.0

New function repSomaticHypermutation() to calculate number of mutations against the germline for each clonotype
Visualization for repGermline() beta: for now, specific clonotypes can be highlighted on the tree only by manually changing values in Type column
All repGermline() options are now starting with . point
repGermline(): .ref_only_first argument removed, because alleles are already unique for each species
New repGermline() option .align_j_gene for more precise (but slower) germline calculation
Updated tutorials
Various updates for texts and documentation
Various bugfixes in BCR pipeline

Immunarch 0.6.9

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

Immunarch 0.6.8

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

Immunarch 0.6.7

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

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