Package: CellaRepertorium 1.15.0

Andrew McDavid

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

Methods to cluster and analyze high-throughput single cell immune cell repertoires, especially from the 10X Genomics VDJ solution. Contains an R interface to CD-HIT (Li and Godzik 2006). Methods to visualize and analyze paired heavy-light chain data. Tests for specific expansion, as well as omnibus oligoclonality under hypergeometric models.

Authors:Andrew McDavid [aut, cre], Yu Gu [aut], Erik VonKaenel [aut], Aaron Wagner [aut], Thomas Lin Pedersen [ctb]

# Install 'CellaRepertorium' in R:

install.packages('CellaRepertorium', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/amcdavid/cellarepertorium/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

ccdb_ex - A preconstructed 'ContigClusterDB' from the 'contigs_qc' data
contigs_qc - Filtered and annotated contigs of TCR from mice

On BioConductor:CellaRepertorium-1.15.0(bioc 3.20)CellaRepertorium-1.14.0(bioc 3.19)

bioconductor-package

44 exports 0.82 score 47 dependencies

Last updated 2 months agofrom:eb648b98f5

Exports:canonicalize_cell canonicalize_cluster ccdb_join cdhit cdhit_ccdb cland cluster_filterset cluster_germline cluster_logistic_test cluster_permute_test cluster_plot cluster_test_by ContigCellDB ContigCellDB_10XVDJ cross_tab_tbl crosstab_by_celltype entropy enumerate_pairing equalize_ccdb fancy_name_contigs filter_cdb fine_cluster_seqs fine_clustering generate_pseudobulk guess_celltype ig_chain_recode left_join_warn map_axis_labels modal_category mutate_cdb np pairing_tables plot_cluster_factors plot_permute_test purity rank_chain_ccdb rank_prevalence_ccdb rbind right_join_warn split_cdb tcr_chain_recode tidy tidy.PermuteTest tidy.PermuteTestList

Dependencies:askpass BiocGenerics Biostrings cli cpp11 crayon curl dplyr fansi forcats generics GenomeInfoDb GenomeInfoDbData glue hms httr IRanges jsonlite lattice lifecycle magrittr Matrix mime openssl pillar pkgconfig plyr prettyunits progress purrr R6 Rcpp reshape2 rlang S4Vectors stringi stringr sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XVector zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Cell permutation tests (internal)	.cluster_permute_test
'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects	dim,ContigCellDB-method dimnames,ContigCellDB-method ncol,ContigCellDB-method nrow,ContigCellDB-method [,ContigCellDB,ANY,missing,ANY-method [,ContigCellDB,ANY,missing-method [[,ContigCellDB,character,missing-method
Access public members of ContigCellDB object.	$,ContigCellDB-method $<-,ContigCellDB-method ContigCellDB-mutate
Find a canonical contig to represent a cell	canonicalize_cell
Find a canonical contig to represent a cluster	canonicalize_cluster
A preconstructed 'ContigClusterDB' from the 'contigs_qc' data	ccdb_ex
Join dataframe or SingleCellExperiment object with ContigCellDB object	ccdb_join
R interface to CDHIT/CDHITest	cdhit
Use 'cdhit()' to cluster a 'ContigCellDB()'	cdhit_ccdb
Cluster "And" intersection	cland
A filtration of clusters	cluster_filterset
Cluster contigs by germline properties	cluster_germline
Tests for independence between labels and covariates using permutation of cells	cluster_permute_test
Make a plot showing properties of the clustering	cluster_plot
Test clusters for differential usage	cluster_logistic_test cluster_test_by
Construct a ContigCellDB	ContigCellDB ContigCellDB_10XVDJ
Filtered and annotated contigs of TCR from mice	contigs_qc
Generate a 2d cross tab using arbitrary numbers of columns as factors	cross_tab_tbl
Count contig UMIs by celltype	crosstab_by_celltype
Calculate the entropy of a vector	entropy modal_category np
Take the intersection of keys in tables in 'x'	equalize_ccdb
Generate a legible name for a series of contigs	fancy_name_contigs
Create new or update existing columns of 'ContigCellDB' tables	filter_cdb mutate_cdb
Calculate distances and perform hierarchical clustering on a set of sequences	fine_cluster_seqs
Perform additional clustering of sequences within groups	fine_clustering
Generate "pseudobulk" data from a 'ContigCellDB'	generate_pseudobulk
Guess the cell type of a contig from the chain ID	guess_celltype
Selectively muffle warnings based on output	hushWarning
Categorize the pairing present in a cell	enumerate_pairing ig_chain_recode tcr_chain_recode
Color axis labels	map_axis_labels
Generate a list of tables representing clusters paired in cells	pairing_tables
Visualization of pairs of cluster factor	plot_cluster_factors
Plot a histogram of permuted vs observed test statistic	plot_permute_test print.PermuteTest print.PermuteTestList tidy.PermuteTest tidy.PermuteTestList
Calculate number of cluster-subject singletons for the purposes of permutation testing	purity
Rank contigs, per cell, by experiment-wide prevalence of 'cluster_pk', which is added as the 'prevalence' field	rank_chain_ccdb rank_prevalence_ccdb
Combine 'ContigCellDB' along rows (contigs, cells or clusters).	rbind,ContigCellDB-method rbind.ContigCellDB
Turn an object into a tidy tibble	reexports tidy
Perform a 'dplyr::left_join()' but check for non-key overlapping fields	left_join_warn right_join_warn
Split into a list of 'ContigCellDB()' by named fields	split_cdb

Package: CellaRepertorium 1.15.0

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

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