Package: Platypus 3.6.0

Alexander Yermanos

Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.

Authors:Alexander Yermanos [aut, cre], Andreas Agrafiotis [ctb], Victor Kreiner [ctb], Tudor-Stefan Cotet [ctb], Raphael Kuhn [ctb], Danielle Shlesinger [ctb], Jiami Han [ctb], Vittoria Martinolli D'Arcy [ctb], Lucas Stalder [ctb], Daphne van Ginneken [ctb]

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Platypus.pdf |Platypus.html✨
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NEWS

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

Peer review:

Datasets:
  • small_vdj - Small VDJ dataframe for function testing purposes
  • small_vgm - Small VDJ GEX matrix (VGM) for function testing purposes

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.60 score 40 scripts 94 downloads 218 mentions 63 exports 173 dependencies

Last updated 5 days agofrom:9d71944457. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 19 2024
R-4.5-linuxOKOct 19 2024

Exports:GEX_cluster_genesGEX_cluster_genes_heatmapGEX_cluster_membershipGEX_coexpression_coefficientGEX_DEgenesGEX_dottile_plotGEX_gene_visualizationGEX_GSEAGEX_heatmapGEX_lineage_trajectoriesGEX_pairwise_DEGsGEX_phenotypeGEX_phenotype_per_cloneGEX_proportions_barplotGEX_scatter_coexpressionGEX_volcanoPlatypusDB_AIRR_to_VGMPlatypusDB_load_from_diskPlatypusDB_VGM_to_AIRRVDJ_abundancesVDJ_alpha_beta_Vgene_circosVDJ_antigen_integrateVDJ_assemble_for_PnPVDJ_buildVDJ_call_encloneVDJ_circosVDJ_clonal_barplotVDJ_clonal_donutVDJ_clonal_expansionVDJ_clonotypeVDJ_clonotype_v3_w_encloneVDJ_contigs_to_vgmVDJ_db_annotateVDJ_db_loadVDJ_diversityVDJ_dynamicsVDJ_expand_aberrantsVDJ_extract_germline_consensus_refVDJ_germlineVDJ_get_publicVDJ_GEX_clonotype_clusters_circosVDJ_GEX_matrixVDJ_GEX_overlay_clonesVDJ_GEX_statsVDJ_kmersVDJ_logoplot_vectorVDJ_networkVDJ_ordinationVDJ_overlap_heatmapVDJ_phylogenetic_treesVDJ_phylogenetic_trees_plotVDJ_plot_SHMVDJ_publicVDJ_rarefactionVDJ_variants_per_cloneVDJ_Vgene_usageVDJ_Vgene_usage_barplotVDJ_Vgene_usage_stacked_barplotVDJ_VJ_usage_circosVGM_buildVGM_expand_featurebarcodesVGM_expanded_clonesVGM_integrate

Dependencies:abindade4apeaplotaskpassassertthatbase64encBHBiocGenericsBiostringsbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataggalluvialggfunggplot2ggplotifyggrepelggridgesggseqlogoggtreeglobalsgluegoftestgplotsgridExtragridGraphicsgtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpixmappkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS4VectorssassscalesscattermoresctransformsegmentedseqinrSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringdiststringistringrsurvivalsystensortibbletidyrtidyselecttidytreetinytextreeioUCSC.utilsusefulutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlyulab.utilszlibbioczoo

PlatypusV3 AgedCNS vignette

Alexander Yermanos, Victor Kreiner, Andreas Agrafiotis, Tudor-Stefan Cotet

Rendered fromPlatypusV3_agedCNS.Rmdusingknitr::rmarkdownon Oct 19 2024.

Last update: 2024-02-22
Started: 2021-10-19

Readme and manuals

Help Manual

Help pageTopics
Differentially expressed genes between clusters or data subsetsGEX_cluster_genes
Heatmap of cluster defining genesGEX_cluster_genes_heatmap
Cluster membership plots by sampleGEX_cluster_membership
Coexpression of selected genesGEX_coexpression_coefficient
Wrapper for differential gene expression analysis and plottingGEX_DEgenes
GEX Dottile plotsGEX_dottile_plot
Visualization of marker expression in a data set or of predefined genes (B cells, CD4 T cells and CD8 T cells).GEX_gene_visualization
GEX Gene Set Enrichment Analysis and plottingGEX_GSEA
Flexible GEX heatmap wrapperGEX_heatmap
This is a function to infer single cell trajectories and identifying lineage structures on clustered cells. Using the slingshot libraryGEX_lineage_trajectories
Wrapper for calculating pairwise differentially expressed genesGEX_pairwise_DEGs
Assignment of cells to phenotypes based on selected markersGEX_phenotype
Plotting of GEX phenotype by VDJ cloneGEX_phenotype_per_clone
Plots proportions of a group of cells within a secondary group of cells. E.g. The proportions of samples in seurat clusters, or the proportions of samples in defined cell subtypesGEX_proportions_barplot
Scatter plot for coexpression of two selected genesGEX_scatter_coexpression
Flexible wrapper for GEX volcano plotsGEX_volcano
AIRR to Platypus V3 VGM compatibility functionPlatypusDB_AIRR_to_VGM
PlatypusDB utility for import of local datasetsPlatypusDB_load_from_disk
Platypus V3 VGM to AIRR compatibility functionPlatypusDB_VGM_to_AIRR
Small VDJ dataframe for function testing purposessmall_vdj
Small VDJ GEX matrix (VGM) for function testing purposessmall_vgm
Calculate abundances/counts of specific features for a VDJ dataframeVDJ_abundances
Produces a Circos plot from the VDJ_analyze output. Connects the V-alpha with the corresponding V-beta gene for each clonotype.VDJ_alpha_beta_Vgene_circos
Integrates antigen-specific information into the VDJ/VDJ.GEX.matrix[[1]] objectVDJ_antigen_integrate
Ab sequence assembly for recombinant PnP expressionVDJ_assemble_for_PnP
Minimal Version of the VDJ Building Part from VDJ_GEX_matrix() FunctionVDJ_build
(Re)clonotype a VDJ object using cellranger's enclone toolVDJ_call_enclone
Plots a Circos diagram from an adjacency matrix. Uses the Circlize chordDiagram function. Is called by VDJ_clonotype_clusters_circos(), VDJ_alpha_beta_Vgene_circos() and VDJ_VJ_usage_circos() functions or works on its own when supplied with an adjacency matrix.VDJ_circos
Function to create stacked barplots to visualize clonal expansion per repertoire directly from a VDJ matrix (either from the minimal_VDJ() or VDJ_GEX_matrix())VDJ_clonal_barplot
Circular VDJ expansion plotsVDJ_clonal_donut
Flexible wrapper for clonal expansion barplots by isotype, GEX cluster etc.VDJ_clonal_expansion
Platypus V3 clonotyping wrapperVDJ_clonotype
Updated clonotyping function based on implications for cells with different chain numbers than 1 VDJ 1 VJ chains.VDJ_clonotype_v3_w_enclone
Formats "VDJ_contigs_annotations.csv" files from cell ranger to match the VDJ_GEX_matrix output using only cells with 1VDJ and 1VJ chainVDJ_contigs_to_vgm
Wrapper function of VDJ_antigen_integrate functionVDJ_db_annotate
Load and preprocess a list of antigen-specific databasesVDJ_db_load
Calculates and plots common diversity and overlap measures for repertoires and alike. Requires the vegan packageVDJ_diversity
Tracks a specific VDJ column across multiple samples/timepoints.VDJ_dynamics
Expand the aberrant cells in a VDJ dataframe by converting them into additional rowsVDJ_expand_aberrants
Making the trimmed reference and concatenating fr1-fr4VDJ_extract_germline_consensus_ref
Infer germline from the desired software/callerVDJ_germline
Function to get shared/public elements across multiple repertoiresVDJ_get_public
Makes a Circos plot from the VDJ_GEX_integrate output. Connects the clonotypes with the corresponding clusters.VDJ_GEX_clonotype_clusters_circos
VDJ GEX processing and integration wrapperVDJ_GEX_matrix
Overlay clones on GEX projectionVDJ_GEX_overlay_clones
Standalone VDJ and GEX statistics.VDJ_GEX_stats
Calculates and plots kmers distributions and frequencies.VDJ_kmers
Flexible logoplot wrapperVDJ_logoplot_vector
Similarity networks based on CDR3 regionsVDJ_network
Performs ordination/dimensionality reduction for a species incidence matrix, depending on the species selected in the feature.columns parameter.VDJ_ordination
Wrapper to determine and plot overlap between VDJ features across groupsVDJ_overlap_heatmap
Creates phylogenetic trees from a VDJ dataframeVDJ_phylogenetic_trees
Phylogenetic tree plottingVDJ_phylogenetic_trees_plot
Plotting of somatic hypermutation countsVDJ_plot_SHM
Function to get shared/public elements across multiple repertoiresVDJ_public
Plots rarefaction curves for species denoted in the feature.columns parameter across groups determined by grouping.columnsVDJ_rarefaction
Wrapper for variant analysis by cloneVDJ_variants_per_clone
V(D)J gene usage stacked barplotsVDJ_Vgene_usage
V(D)J gene usage barplotsVDJ_Vgene_usage_barplot
V(D)J gene usage stacked barplotsVDJ_Vgene_usage_stacked_barplot
Makes a Circos plot from the VDJ_analyze output. Connects the V gene with the corresponding J gene for each clonotype.VDJ_VJ_usage_circos
Function to obtain the VGM object by integrating the VDJ and GEX/Seurat objectsVGM_build
Utility for feature barcode assignment including clonal informationVGM_expand_featurebarcodes
VDJ utility for T/F column for clonal expansionVGM_expanded_clones
Utility for VDJ GEX matrix to integrated VDJ and GEX objects after addition of data to eitherVGM_integrate