Files in immunomind/immunarch
Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
.Rbuildignore
.dockerignore
.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
.github/workflows/dockerhub.yml
.gitignore
CONTRIBUTION.md
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
NEWS.md
R/RcppExports.R
R/align_lineage.R
R/annotation.R
R/clonality.R
R/clustering.R
R/data_docs.R
R/dimensions.R
R/distance.R
R/diversity.R
R/dynamics.R
R/explore.R
R/filters.R
R/gene_usage.R
R/gene_usage_analysis.R
R/germline.R
R/immunarch-package.R
R/immunarch-remaster.R
R/immunr_data_format.R
R/info_theory.R
R/io-parsers.R
R/io-savers.R
R/io-utility.R
R/io.R
R/kmers.R
R/overlap.R
R/overlap_analysis.R
R/phylip.R
R/preprocessing.R
R/public.R
R/sampling.R
R/seqCluster.R
R/shiny.R
R/singlecell.R
R/somatic_hypermutation.R
R/spectratyping.R
R/tools.R
R/vis.R
README.md
_pkgdown.yml
code-of-conduct.md
data/aaproperties.rda
data/bcrdata.rda
data/genesegments.rda
data/immdata.rda
data/nonbuild/ms.rda
data/nonbuild/ms_small.rda
data/nonbuild/test.rda
data/nonbuild/test2.rda
data/scdata.rda
fixVis/app.R
immunarch-citation.xml
immunr.Rproj
inst/extdata/db/vdjdb.example.txt
inst/extdata/io/Sample1.tsv.gz
inst/extdata/io/Sample2.tsv.gz
inst/extdata/io/Sample3.tsv.gz
inst/extdata/io/Sample4.tsv.gz
inst/extdata/io/metadata.txt
inst/extdata/sc/flu.csv.gz
man/aa_properties.Rd
man/aa_table.Rd
man/add_class.Rd
man/apply_symm.Rd
man/bcrdata.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/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/pubRep.Rd
man/pubRepApply.Rd
man/pubRepFilter.Rd
man/pubRepStatistics.Rd
man/public_matrix.Rd
man/repAlignLineage.Rd
man/repClonalFamily.Rd
man/repClonality.Rd
man/repDiversity.Rd
man/repExplore.Rd
man/repFilter.Rd
man/repGermline.Rd
man/repLoad.Rd
man/repOverlap.Rd
man/repOverlapAnalysis.Rd
man/repSample.Rd
man/repSave.Rd
man/repSomaticHypermutation.Rd
man/scdata.Rd
man/select_barcodes.Rd
man/select_clusters.Rd
man/seqCluster.Rd
man/seqDist.Rd
man/set_pb.Rd
man/spectratype.Rd
man/split_to_kmers.Rd
man/switch_type.Rd
man/top.Rd
man/trackClonotypes.Rd
man/vis.Rd
man/vis.clonal_family.Rd
man/vis.clonal_family_tree.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.step_failure_ignored.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_textlogo.Rd
pkgdown/extra.css
src/.gitignore
src/RcppExports.cpp
src/fill_functions.cpp
tests/.gitignore
tests/test_parsing_data/folder/immunoseq_1.txt
tests/test_parsing_data/folder/immunoseq_2.txt
tests/test_parsing_data/folder/immunoseq_3.txt
tests/test_parsing_data/folder/metadata.txt
tests/test_parsing_data/immunoseq_1.txt
tests/test_parsing_data/immunoseq_2.txt
tests/test_parsing_data/immunoseq_3.txt
tests/test_parsing_data/immunoseq_4.txt
tests/testthat.R
tests/testthat/helper-preload.R
tests/testthat/test-align-lineage.R
tests/testthat/test-clonal-family.R
tests/testthat/test-clonality.R
tests/testthat/test-distance.R
tests/testthat/test-diversity.R
tests/testthat/test-dynamics.R
tests/testthat/test-explore.R
tests/testthat/test-filter.R
tests/testthat/test-geneusage.R
tests/testthat/test-germline.R
tests/testthat/test-kmers.R
tests/testthat/test-overlap.R
tests/testthat/test-pubrep.R
tests/testthat/test-seqCluster.R
tests/testthat/test-somatic-hypermutation.R
tests/testthat/test-spectr.R
vignettes/v1_introduction.Rmd
vignettes/v2_data.Rmd
vignettes/web_only/BCRpipeline.Rmd
vignettes/web_only/clustering.Rmd
vignettes/web_only/community.Rmd
vignettes/web_only/load_10x.Rmd
vignettes/web_only/load_mixcr.Rmd
vignettes/web_only/repFilter_v3.Rmd
vignettes/web_only/v10_prop.Rmd
vignettes/web_only/v11_db.Rmd
vignettes/web_only/v21_singlecell.Rmd
vignettes/web_only/v3_basic_analysis.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
