Package: VDJdive 1.9.0

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_1.9.0.tar.gz
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VDJdive.pdf |VDJdive.html✨
VDJdive/json (API)
NEWS

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

Peer review:

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-1.9.0(bioc 3.21)VDJdive-1.8.0(bioc 3.20)

softwareimmunooncologysinglecellannotationrnaseqtargetedresequencing

5.32 score 7 stars 1 scripts 136 downloads 20 exports 67 dependencies

Last updated 19 days agofrom:9a1d59527c. Checks:OK: 1 NOTE: 3 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64WARNINGOct 31 2024
R-4.5-linux-x86_64NOTEOct 31 2024
R-4.4-win-x86_64WARNINGOct 31 2024
R-4.4-mac-x86_64WARNINGOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64WARNINGOct 31 2024
R-4.3-mac-x86_64WARNINGOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

Exports:abundanceVDJaddVDJtoSCEbarVDJboxVDJcalculateDiversityclonoAbundanceclonoAssignmentclonoFrequencyclonoGroupclonoNamesclonoStatspieVDJreadVDJcontigsrunBreakawayrunVDJPCAscatterVDJshowsplitClonotypessummarizeClonotypeswriteVDJcontigs

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArrayfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcpprlangS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

VDJdive Workflow

Kelly Street, Mercedeh Movassagh, Jill Lundell

Rendered fromworkflow.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Create an abundance graph for clonotype expansionabundanceVDJ abundanceVDJ,clonoStats-method
Add 10X CellRanger V(D)J data to SingleCellExperimentaddVDJtoSCE addVDJtoSCE,character,SingleCellExperiment-method addVDJtoSCE,SplitDataFrameList,SingleCellExperiment-method
Create a bar graph for clonotype expansionbarVDJ barVDJ,clonoStats-method barVDJ,Matrix-method barVDJ,matrix-method
Create a box plot for diversity measuresboxVDJ boxVDJ,matrix-method
Sample diversity estimationcalculateDiversity calculateDiversity,clonoStats-method calculateDiversity,SingleCellExperiment-method
Assign cell-level clonotypes and calculate abundancesclonoStats clonoStats,clonoStats-method clonoStats,SingleCellExperiment-method clonoStats,SplitDataFrameList-method
'clonoStats' object classclonoAbundance 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 cellscontigs
Create a pie chart for clonotype expansionpieVDJ pieVDJ,clonoStats-method pieVDJ,Matrix-method pieVDJ,matrix-method
Load 10X CellRanger V(D)J datareadVDJcontigs readVDJcontigs,character-method
Clonotype richness estimation with BreakawayrunBreakaway runBreakaway,clonoStats-method
Run PCA on clonotype abundance matrixrunVDJPCA runVDJPCA,clonoStats-method
Create a scatterplot for diversity evenness and abundancescatterVDJ scatterVDJ,matrix-method
Split cell-level clonotype counts by samplesplitClonotypes splitClonotypes,clonoStats-method splitClonotypes,Matrix-method splitClonotypes,matrix-method splitClonotypes,SingleCellExperiment-method
Get sample-level clonotype countssummarizeClonotypes summarizeClonotypes,clonoStats-method summarizeClonotypes,Matrix-method summarizeClonotypes,matrix-method summarizeClonotypes,SingleCellExperiment-method
Write V(D)J contig data in 10X formatwriteVDJcontigs writeVDJcontigs,character,SplitDataFrameList-method