Package: VDJdive 1.15.1

Kelly Street

VDJdive: Analysis Tools for 10X V(D)J Data

This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.

Authors:Kelly Street [aut, cre], Mercedeh Movassagh [aut], Jill Lundell [aut], Jared Brown [ctb], Linglin Huang [ctb], Mingzhi Ye [ctb]

VDJdive_1.15.1.tar.gz
VDJdive_1.15.1.zip(r-4.7)VDJdive_1.15.1.zip(r-4.6)VDJdive_1.15.1.zip(r-4.5)
VDJdive_1.15.1.tgz(r-4.6-x86_64)VDJdive_1.15.1.tgz(r-4.6-arm64)VDJdive_1.15.1.tgz(r-4.5-x86_64)VDJdive_1.15.1.tgz(r-4.5-arm64)
VDJdive_1.15.1.tar.gz(r-4.7-arm64)VDJdive_1.15.1.tar.gz(r-4.7-x86_64)VDJdive_1.15.1.tar.gz(r-4.6-arm64)VDJdive_1.15.1.tar.gz(r-4.6-x86_64)
VDJdive_1.15.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
VDJdive/json (API)

# Install 'VDJdive' in R:

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

Bug tracker:https://github.com/kstreet13/vdjdive/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

contigs - SplitDataFrameList containing AIRR-seq (TCR) data for six cells

On BioConductor:VDJdive-1.15.1(bioc 3.24)VDJdive-1.14.0(bioc 3.23)

software immunooncology singlecell annotation rnaseq targetedresequencing cpp

5.77 score 13 stars 2 scripts 279 downloads 20 exports 46 dependencies

Last updated from:e6b1f6bd74. Checks:12 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	230
linux-devel-arm64	NOTE	321
linux-devel-x86_64	NOTE	329
source / vignettes	OK	303
linux-release-arm64	NOTE	351
linux-release-x86_64	NOTE	450
macos-release-arm64	NOTE	300
macos-release-x86_64	NOTE	471
macos-oldrel-arm64	NOTE	197
macos-oldrel-x86_64	NOTE	390
windows-devel	NOTE	301
windows-release	NOTE	250
windows-oldrel	NOTE	305
wasm-release	OK	174

Exports:abundanceVDJ addVDJtoSCE barVDJ boxVDJ calculateDiversity clonoAbundance clonoAssignment clonoFrequency clonoGroup clonoNames clonoStats pieVDJ readVDJcontigs runBreakaway runVDJPCA scatterVDJ show splitClonotypes summarizeClonotypes writeVDJcontigs

Dependencies:abind BH Biobase BiocGenerics BiocParallel cli codetools cowplot cpp11 DelayedArray farver formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gridExtra gtable IRanges isoband labeling lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment snow SparseArray SummarizedExperiment vctrs viridisLite withr XVector

VDJdive Workflow

Rendered fromworkflow.Rmdusingknitr::rmarkdown

Last update: 2023-05-04
Started: 2022-02-14

Help page	Topics
Create an abundance graph for clonotype expansion	abundanceVDJ abundanceVDJ,clonoStats-method
Add 10X CellRanger V(D)J data to SingleCellExperiment	addVDJtoSCE addVDJtoSCE,character,SingleCellExperiment-method addVDJtoSCE,SplitDataFrameList,SingleCellExperiment-method
Create a bar graph for clonotype expansion	barVDJ barVDJ,clonoStats-method barVDJ,Matrix-method barVDJ,matrix-method
Create a box plot for diversity measures	boxVDJ boxVDJ,matrix-method
Sample diversity estimation	calculateDiversity calculateDiversity,clonoStats-method calculateDiversity,SingleCellExperiment-method
Assign cell-level clonotypes and calculate abundances	clonoStats clonoStats,clonoStats-method clonoStats,SingleCellExperiment-method clonoStats,SplitDataFrameList-method
'clonoStats' object class	clonoAbundance clonoAbundance,clonoStats-method clonoAbundance,SingleCellExperiment-method clonoAssignment clonoAssignment,clonoStats-method clonoAssignment,SingleCellExperiment-method clonoFrequency clonoFrequency,clonoStats-method clonoFrequency,SingleCellExperiment-method clonoGroup clonoGroup,clonoStats-method clonoGroup,SingleCellExperiment-method clonoNames clonoNames,clonoStats-method clonoNames,SingleCellExperiment-method clonoStats-class show,clonoStats-method
SplitDataFrameList containing AIRR-seq (TCR) data for six cells	contigs
Create a pie chart for clonotype expansion	pieVDJ pieVDJ,clonoStats-method pieVDJ,Matrix-method pieVDJ,matrix-method
Load 10X CellRanger V(D)J data	readVDJcontigs readVDJcontigs,character-method
Clonotype richness estimation with Breakaway	runBreakaway runBreakaway,clonoStats-method
Run PCA on clonotype abundance matrix	runVDJPCA runVDJPCA,clonoStats-method
Create a scatterplot for diversity evenness and abundance	scatterVDJ scatterVDJ,matrix-method
Split cell-level clonotype counts by sample	splitClonotypes splitClonotypes,clonoStats-method splitClonotypes,Matrix-method splitClonotypes,matrix-method splitClonotypes,SingleCellExperiment-method
Get sample-level clonotype counts	summarizeClonotypes summarizeClonotypes,clonoStats-method summarizeClonotypes,Matrix-method summarizeClonotypes,matrix-method summarizeClonotypes,SingleCellExperiment-method
Write V(D)J contig data in 10X format	writeVDJcontigs writeVDJcontigs,character,SplitDataFrameList-method

Package: VDJdive 1.15.1

VDJdive: Analysis Tools for 10X V(D)J Data

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Help Manual

Usage by other packages (reverse dependencies)