Files in CellaRepertorium

Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

NEWS.md README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

src/progress.h

src/cdhit-common.h

src/cdhit-est.cpp

src/RcppExports.cpp

src/cdhit-common.cpp

src/progress.cpp

src/cdhit-bombs.cpp

src/cdhit.cpp

data/ccdb_ex.rda

data/contigs_qc.rda

R/cdhit-methods.R R/auxiliary.R R/RcppExports.R R/utilty.R R/cluster-testing.R R/vdjcellranger-methods.R R/pairing-methods.R R/ccdb_join.R R/plotting.R R/permutation-testing.R R/pseudo-bulk.R R/AllClasses.R R/clustering-methods.R R/data.R R/ggplot2-utils.R R/ContigCellDB-methods.R

vignettes/citations.bib

vignettes/mouse_tcell_qc.Rmd vignettes/repertoire_and_expression.Rmd vignettes/cdr3_clustering.Rmd vignettes/cr-overview.Rmd man/cluster_filterset.Rd man/crosstab_by_celltype.Rd man/fancy_name_contigs.Rd man/cluster_permute_test.Rd man/mutate_cdb.Rd man/fine_clustering.Rd man/enumerate_pairing.Rd man/cluster_germline.Rd man/cluster_logistic_test.Rd man/cluster_plot.Rd man/ccdb_join.Rd man/entropy.Rd man/rbind-ContigCellDB-method.Rd man/map_axis_labels.Rd man/cdhit_ccdb.Rd man/guess_celltype.Rd man/purity.Rd man/canonicalize_cluster.Rd man/ccdb_ex.Rd man/hushWarning.Rd man/left_join_warn.Rd man/sub-sub-ContigCellDB-character-missing-method.Rd man/split_cdb.Rd man/generate_pseudobulk.Rd man/cash-ContigCellDB-method.Rd man/cdhit.Rd man/contigs_qc.Rd man/ContigCellDB-fun.Rd man/equalize_ccdb.Rd man/dot-cluster_permute_test.Rd man/fine_cluster_seqs.Rd man/rank_prevalence_ccdb.Rd man/canonicalize_cell.Rd man/pairing_tables.Rd

man/figures/construct_mutate.png

man/figures/contig_schematic.png

man/figures/table_schematic.png

man/figures/VDJ_recombination.png

tests/testthat.R tests/testthat/test-cdhit-methods.R tests/testthat/test-clustering-methods.R tests/testthat/test-ContigCellDB-methods.R tests/testthat/test-ccdb_join.R tests/testthat/test-pairing-methods.R tests/testthat/test-permutation-testing.R tests/testthat/test-cluster-testing.R

tests/testthat/out/pairing1.rda

tests/testthat/out/pairing2.rda

tests/testthat/out/permutation1.rda

tests/testthat/out/pairing3.rda

inst/WORDLIST

inst/doc/mouse_tcell_qc.html

inst/doc/cr-overview.R inst/doc/repertoire_and_expression.R

inst/doc/cdr3_clustering.html

inst/doc/mouse_tcell_qc.Rmd

inst/doc/repertoire_and_expression.html

inst/doc/mouse_tcell_qc.R inst/doc/repertoire_and_expression.Rmd inst/doc/cdr3_clustering.Rmd

inst/doc/cr-overview.html

inst/doc/cdr3_clustering.R inst/doc/cr-overview.Rmd

inst/extdata/all_contig_annotations_balbc_2.json.xz

inst/extdata/all_contig_annotations_balbc_3.csv.xz

inst/extdata/all_contig_annotations_b6_5.json.xz

inst/extdata/all_contig_annotations_b6_4.json.xz

inst/extdata/all_contig_annotations_balbc_2.csv.xz

inst/extdata/all_contig_annotations_b6_4.csv.xz

inst/extdata/all_contig_annotations_b6_5.csv.xz

inst/extdata/all_contig_annotations_b6_6.csv.xz

inst/extdata/all_contig_annotations_balbc_1.csv.xz

inst/extdata/all_contig_annotations_b6_6.json.xz

inst/extdata/all_contig_annotations_balbc_3.json.xz

inst/extdata/demo.fasta

inst/extdata/all_contig_annotations_balbc_1.json.xz

inst/script/10XMouseTCR_v3_chem.R inst/examples/small_cluster_example.R

inst/examples/README

CellaRepertorium documentation built on Nov. 8, 2020, 7:48 p.m.