charlotterich/immunarch_code
Painless Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires in R

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charlotterich/immunarch_code: Painless Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires in R
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Painless Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires in R

.github/ISSUE_TEMPLATE/bug-report.md .github/ISSUE_TEMPLATE/documentation.md .github/ISSUE_TEMPLATE/email-template.md .github/ISSUE_TEMPLATE/feature-request.md .github/ISSUE_TEMPLATE/questions-help-support.md
.gitignore
CNAME
DESCRIPTION
NAMESPACE
NEWS.md R/RcppExports.R R/aa_properties.R R/clonality.R R/clustering.R R/data.R R/data_docs.R R/db.R R/dimensions.R R/diversity.R R/dynamics.R R/explore.R R/gene_usage.R R/gene_usage_analysis.R R/graph.R R/immunarch-package.R R/immunr_data_format.R R/info_theory.R R/io.R R/kmers.R R/metadata.R R/overlap.R R/overlap_analysis.R R/parallel.R R/post_analysis.R R/processing.R R/search.R R/shared.R R/shiny.R R/spectratyping.R R/stat_tests.R R/testing.R R/tools.R R/vis.R README.md
build/vignette.rds
data/aaproperties.rda
data/datalist
data/genesegments.rda
data/immdata.rda
docs/404.html
docs/CNAME
docs/CONTRIBUTION.html
docs/LICENSE-text.html
docs/articles/index.html
docs/articles/v1_introduction.html
docs/articles/v2_data.html
docs/articles/v3_basic_analysis.html
docs/articles/v3_basic_analysis_files/figure-html/clonality-hom-vis-1-1.png
docs/articles/v3_basic_analysis_files/figure-html/clonality-hom-vis-1-2.png
docs/articles/v3_basic_analysis_files/figure-html/clonality-hom-vis-1-3.png
docs/articles/v3_basic_analysis_files/figure-html/eda-1-1.png
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docs/articles/v3_basic_analysis_files/figure-html/eda-by-meta-1.png
docs/articles/v3_basic_analysis_files/figure-html/eda-by-only-1.png
docs/articles/web_only/v10_prop.html
docs/articles/web_only/v11_db.html
docs/articles/web_only/v4_overlap.html
docs/articles/web_only/v4_overlap_files/figure-html/overlap-1-1.png
docs/articles/web_only/v4_overlap_files/figure-html/overlap-1.png
docs/articles/web_only/v4_overlap_files/figure-html/overlap-2-1.png
docs/articles/web_only/v4_overlap_files/figure-html/overlap-2-2.png
docs/articles/web_only/v4_overlap_files/figure-html/overlap-2.png
docs/articles/web_only/v4_overlap_files/figure-html/overlap-signif-digits-1.png
docs/articles/web_only/v5_gene_usage.html
docs/articles/web_only/v5_gene_usage_files/figure-html/spectr-1.png
docs/articles/web_only/v5_gene_usage_files/figure-html/unnamed-chunk-10-1.png
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docs/articles/web_only/v5_gene_usage_files/figure-html/unnamed-chunk-9-1.png
docs/articles/web_only/v6_diversity.html
docs/articles/web_only/v6_diversity_files/figure-html/diversity-1.png
docs/articles/web_only/v6_diversity_files/figure-html/diversity-2.png
docs/articles/web_only/v6_diversity_files/figure-html/diversity-3.png
docs/articles/web_only/v6_diversity_files/figure-html/unnamed-chunk-1-1.png
docs/articles/web_only/v7_fixvis.html
docs/articles/web_only/v8_tracking.html
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docs/articles/web_only/v8_tracking_files/figure-html/unnamed-chunk-8-3.png
docs/articles/web_only/v9_kmers.html
docs/articles/web_only/v9_kmers_files/figure-html/unnamed-chunk-10-1.png
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docs/articles/web_only/v9_kmers_files/figure-html/unnamed-chunk-7-1.png
docs/authors.html
docs/code-of-conduct.html
docs/docsearch.css
docs/docsearch.js
docs/docsearch.json
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/aa_properties.html
docs/reference/aa_table.html
docs/reference/add_class.html
docs/reference/apply_symm.html
docs/reference/bunch_translate.html
docs/reference/check_distribution.html
docs/reference/coding.html
docs/reference/dbAnnotate.html
docs/reference/dbLoad.html
docs/reference/dot-quant_column_choice.html
docs/reference/entropy.html
docs/reference/filter_barcodes.html
docs/reference/fixVis.html
docs/reference/geneUsage.html
docs/reference/geneUsageAnalysis.html
docs/reference/gene_segments.html
docs/reference/gene_stats.html
docs/reference/getKmers.html
docs/reference/group_from_metadata.html
docs/reference/has_class.html
docs/reference/immdata.html
docs/reference/immunr_data_format.html
docs/reference/immunr_hclust.html
docs/reference/immunr_pca.html
docs/reference/inc_overlap.html
docs/reference/index.html
docs/reference/matrixdiagcopy.html
docs/reference/num_shared_clonotypes.html
docs/reference/overlap_coef.html
docs/reference/pubRep.html
docs/reference/pubRepApply.html
docs/reference/pubRepFilter.html
docs/reference/pubRepStatistics.html
docs/reference/public_matrix.html
docs/reference/repClonality.html
docs/reference/repDiversity.html
docs/reference/repExplore.html
docs/reference/repLoad.html
docs/reference/repOverlap.html
docs/reference/repOverlapAnalysis.html
docs/reference/repSample.html
docs/reference/repSave.html
docs/reference/set_pb.html
docs/reference/spectratype.html
docs/reference/split_immunoseq_files.html
docs/reference/split_to_kmers.html
docs/reference/switch_type.html
docs/reference/top.html
docs/reference/trackClonotypes.html
docs/reference/vis.html
docs/reference/vis.immunr_chao1.html
docs/reference/vis.immunr_clonal_prop.html
docs/reference/vis.immunr_dynamics.html
docs/reference/vis.immunr_exp_vol.html
docs/reference/vis.immunr_gene_usage.html
docs/reference/vis.immunr_hclust.html
docs/reference/vis.immunr_inc_overlap.html
docs/reference/vis.immunr_kmeans.html
docs/reference/vis.immunr_kmer_table.html
docs/reference/vis.immunr_mds.html
docs/reference/vis.immunr_ov_matrix.html
docs/reference/vis.immunr_public_repertoire.html
docs/reference/vis.immunr_public_statistics.html
docs/reference/vis_bar.html
docs/reference/vis_box.html
docs/reference/vis_circos.html
docs/reference/vis_heatmap.html
docs/reference/vis_heatmap2.html
docs/reference/vis_hist.html
docs/reference/vis_immunr_kmer_profile_main.html
docs/reference/vis_public_clonotypes.html
docs/reference/vis_public_frequencies.html
docs/reference/vis_radar.html
docs/reference/vis_textlogo.html
docs/reference/vis_treemap.html
docs/sitemap.xml
immunarch.tar.gz
inst/doc/v1_introduction.R inst/doc/v1_introduction.Rmd
inst/doc/v1_introduction.html
inst/doc/v2_data.R inst/doc/v2_data.Rmd
inst/doc/v2_data.html
inst/doc/v3_basic_analysis.R inst/doc/v3_basic_analysis.Rmd
inst/doc/v3_basic_analysis.html
inst/dynamics_analysis.Rmd inst/exploratory_analysis.Rmd inst/intergroup_analysis.Rmd man/aa_properties.Rd man/aa_table.Rd man/add_class.Rd man/apply_symm.Rd man/bunch_translate.Rd man/check_distribution.Rd man/coding.Rd man/dbAnnotate.Rd man/dbLoad.Rd man/dot-quant_column_choice.Rd man/entropy.Rd man/filter_barcodes.Rd man/fixVis.Rd man/geneUsage.Rd man/geneUsageAnalysis.Rd man/gene_segments.Rd man/gene_stats.Rd man/getKmers.Rd man/group_from_metadata.Rd man/has_class.Rd man/immdata.Rd man/immunr_data_format.Rd man/immunr_hclust.Rd man/immunr_pca.Rd man/inc_overlap.Rd man/matrixdiagcopy.Rd man/num_shared_clonotypes.Rd man/overlap_coef.Rd man/pubRep.Rd man/pubRepApply.Rd man/pubRepFilter.Rd man/pubRepStatistics.Rd man/public_matrix.Rd man/repClonality.Rd man/repDiversity.Rd man/repExplore.Rd man/repLoad.Rd man/repOverlap.Rd man/repOverlapAnalysis.Rd man/repSample.Rd man/repSave.Rd man/set_pb.Rd man/spectratype.Rd man/split_immunoseq_files.Rd man/split_to_kmers.Rd man/switch_type.Rd man/top.Rd man/trackClonotypes.Rd man/vis.Rd man/vis.immunr_chao1.Rd man/vis.immunr_clonal_prop.Rd man/vis.immunr_dynamics.Rd man/vis.immunr_exp_vol.Rd man/vis.immunr_gene_usage.Rd man/vis.immunr_hclust.Rd man/vis.immunr_inc_overlap.Rd man/vis.immunr_kmeans.Rd man/vis.immunr_kmer_table.Rd man/vis.immunr_mds.Rd man/vis.immunr_ov_matrix.Rd man/vis.immunr_public_repertoire.Rd man/vis.immunr_public_statistics.Rd man/vis_bar.Rd man/vis_box.Rd man/vis_circos.Rd man/vis_heatmap.Rd man/vis_heatmap2.Rd man/vis_hist.Rd man/vis_immunr_kmer_profile_main.Rd man/vis_public_clonotypes.Rd man/vis_public_frequencies.Rd man/vis_radar.Rd man/vis_textlogo.Rd man/vis_treemap.Rd
src/RcppExports.cpp
src/fill_functions.cpp
vignettes/v1_introduction.Rmd vignettes/v2_data.Rmd vignettes/v3_basic_analysis.Rmd vignettes/web_only/v10_prop.Rmd vignettes/web_only/v11_db.Rmd vignettes/web_only/v4_overlap.Rmd vignettes/web_only/v5_gene_usage.Rmd vignettes/web_only/v6_diversity.Rmd vignettes/web_only/v7_fixvis.Rmd vignettes/web_only/v8_tracking.Rmd vignettes/web_only/v9_kmers.Rmd
charlotterich/immunarch_code documentation built on Jan. 24, 2020, 12:08 a.m.

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