New release: 0.6.4

Author: EugeneRumynskiy

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^docs$
+^data/nonbuild/.*$
+^data/nonbuild/*$
+^tests$
+^twb$
+^temp$
+^fixVis$
+^experiment data$
+^docker$
+^private$
+^.gitlab-ci.yml$
+^CONTRIBUTION.md$
+^_pkgdown.yml$
+^code-of-conduct.md$
+^LICENSE$
+^immunarch-citation.xml$
+^.github$

.gitignore

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-.DS_store
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+src/*.o
+src/*.so
+src/*.dll
+*.DS_Store
+docs/*
+

CNAME

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+# Contributing to immunarch
+
+This outlines how to propose a change to immunarch.
+
+### Fixing typos
+
+Small typos or grammatical errors in documentation may be edited directly using
+the GitLab web IDE functionality / GitHub web interface, so long as the changes are made in the _source_ file.
+
+*  YES: you edit a roxygen comment in a `.R` file below `R/`.
+*  NO: you edit an `.Rd` file below `man/`.
+
+### Prerequisites
+
+Before you make a substantial pull request, you should always file an issue and
+make sure someone from the team agrees that it's a problem. If you've found a
+bug, create an associated issue and illustrate the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex). If you need to send a data and can't do
+that via GitHub, please note it in the issue.
+
+### Pull request process
+
+*  We recommend that you create a Git branch for each pull request (PR).  
+*  Look at the CI (Continuous Integration) build status before and after making changes.
+The `README` should contain badges for any continuous integration services used
+by the package.  
+*  New code should follow our style guide that is the tidyverse [style guide](http://style.tidyverse.org)
+with a very minor addition of using `=` instead of `<-` in variable assignment.
+You can use the [styler](https://CRAN.R-project.org/package=styler) package to
+apply these styles, but please don't restyle code that has nothing to do with 
+your PR.  
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2) for documentation.  
+*  We use [testthat](https://cran.r-project.org/package=testthat). Contributions
+with test cases included are easier to accept.  
+*  For user-facing changes, add a bullet to the top of `NEWS.md` below the current
+development version header describing the changes made followed by your GitHub
+username, and links to relevant issue(s)/PR(s).
+
+### Code of Conduct
+
+Please note that this project is released with a [Contributor Code of
+Conduct](code-of-conduct.md). By participating in this project you agree to
+abide by its terms.
+
+(adapted from [dplyr](https://github.com/tidyverse/dplyr/blob/master/.github/CONTRIBUTING.md) contribution guide)

CONTRIBUTION.md

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+Package: immunarch
+Type: Package
+Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
+Version: 0.6.4
+Authors@R: c(
+    person("Vadim I.", "Nazarov", , "[email protected]", c("aut", "cre")),
+    person("Vasily O.", "Tsvetkov", , role = "aut"),
+    person("Eugene", "Rumynskiy", , role = "aut"),
+    person("Anna", "Lorenc", , role = "aut"),
+    person("Daniel J.", "Moore", , role = "aut"),
+    person("Victor", "Greiff", , role = "aut"),
+    person("ImmunoMind", role = c("cph", "fnd"))
+    )
+Contact: [email protected]
+Description: A comprehensive framework for bioinformatics analysis of bulk and single-cell 
+    T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and 
+    visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq)
+    and single-cell sequencing (scRNAseq). It implements most of the widely used AIRR analysis methods, 
+    such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes 
+    and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor 
+    databases and clonotype tracking in vaccination and cancer studies. A successor to our
+    previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
+License: AGPL-3
+URL: https://immunarch.com/, https://github.com/immunomind/immunarch
+BugReports: https://github.com/immunomind/immunarch/issues
+Imports:
+    pheatmap (>= 1.0.12),
+    ggrepel (>= 0.8.0),
+    reshape2 (>= 1.4.2),
+    factoextra (>= 1.0.4),
+    fpc,
+    circlize,
+    MASS (>= 7.3),
+    Rtsne (>= 0.15),
+    readr (>= 1.3.1),
+    readxl (>= 1.3.1),
+    shiny (>= 1.4.0),
+    shinythemes,
+    treemap,
+    airr,
+    ggseqlogo,
+    UpSetR (>= 1.4.0),
+    stringr (>= 1.4.0),
+    ggalluvial (>= 0.10.0),
+    Rcpp (>= 1.0),
+    magrittr,
+    tibble (>= 2.0),
+    methods,
+    scales,
+    ggpubr (>= 0.2),
+    rlang (>= 0.4),
+    plyr,
+    dbplyr (>= 1.4.0)
+Depends:
+    R (>= 3.5.0),
+    ggplot2 (>= 3.1.0),
+    dplyr (>= 0.8.0),
+    dtplyr (>= 1.0.0),
+    data.table (>= 1.12.6),
+    gridExtra (>= 2.2.1)
+LinkingTo: Rcpp
+Suggests:
+    knitr (>= 1.8),
+    roxygen2 (>= 3.0.0),
+    testthat (>= 2.1.0),
+    pkgdown (>= 0.1.0),
+    assertthat
+VignetteBuilder: knitr
+Encoding: UTF-8
+RoxygenNote: 7.1.0
+LazyData: true