Files in CellaRepertorium
Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
NEWS.md
README.md
CellaRepertorium documentation built on Nov. 8, 2020, 7:48 p.m.
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
