Recent Releases of immunarch
immunarch - Immunarch 0.9.1
What's Changed
- Dev by @vadimnazarov in https://github.com/immunomind/immunarch/pull/403
Full Changelog: https://github.com/immunomind/immunarch/compare/0.9.0...0.9.1
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Published by vadimnazarov about 2 years ago
immunarch - 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
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Published by Alexander230 over 3 years ago
immunarch - 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 .alignjgene from repGermline() and .verboseoutput 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 .trimgenes 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
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Published by Alexander230 over 3 years ago
immunarch - 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(): .refonlyfirst argument removed, because alleles are already unique for each species New repGermline() option .alignjgene for more precise (but slower) germline calculation Updated tutorials Various updates for texts and documentation Various bugfixes in BCR pipeline
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Published by Alexander230 almost 4 years ago
immunarch - 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
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Published by Alexander230 about 4 years ago
immunarch - 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
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Published by Alexander230 about 4 years ago
immunarch - 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 .whichrecombtype 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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Published by Alexander230 over 4 years ago
immunarch - 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 selectbarcodes 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 rawcontig and rawclonotype 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 filterbarcodes() to singlecell.R and rename it to selectbarcodes() 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 datadocs.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 IOREFACTOR 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): addclass() 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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Published by vadimnazarov almost 6 years ago
immunarch - 0.6.4
immunarch is 0.6.4 now!
News
- Updated website with better documentation.
- We embedded email registration on the front page. Get in touch, we are ready to it!
- The package is now could be installed via devtools::install_github("immunomind/immunarch").
Fixed Issues
Comprehensive issue list since 0.5.5.
- R
Published by EugeneRumynskiy about 6 years ago
immunarch - 0.5.5
immunarch 0.5.5
We are 0.5.5 now! This is a minor release.
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- We fixed incorrect parsing of MiXCR for files with ","
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- 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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Published by EugeneRumynskiy over 6 years ago
immunarch - 0.5.4
immunarch 0.5.4
We are 0.5.4 now!
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
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- 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.
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- Clonotype counting is fixed now
Single-cell analysis
- We added a new function filter_barcodes for filtering by barcodes for single-cell data
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- We added Search field to the website to make docs more available for you
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Published by EugeneRumynskiy over 6 years ago
immunarch - 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
- 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
- We added new functions:
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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 quantcolumnchoise from export fix(upkeep): add melt.data.table because otherwise vis.immunedynamics 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
- R
Published by EugeneRumynskiy over 6 years ago
immunarch - 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
- R
Published by EugeneRumynskiy over 6 years ago
immunarch - 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.tablesproperly - fix(io): fix a bug when
.compress=Fdoesn't work inrepSaveif.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
.codingdoesn'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
- R
Published by EugeneRumynskiy almost 7 years ago
immunarch - 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.
- R
Published by vadimnazarov almost 7 years ago
immunarch - 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.
- R
Published by vadimnazarov almost 7 years ago