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Platypus  

Single-Cell Immune Repertoire and Gene Expression Analysis
View on CRAN: Click here


Download and install Platypus package within the R console
Install from CRAN:
install.packages("Platypus")

Install from Github:
library("remotes")
install_github("cran/Platypus")

Install by package version:
library("remotes")
install_version("Platypus", "3.5.0")



Attach the package and use:
library("Platypus")
Maintained by
Alexander Yermanos
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-10-19
Latest Update: 2024-02-21
Description:
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) , Cotet et al. (2023) .
How to cite:
Alexander Yermanos (2021). Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis. R package version 3.5.0, https://cran.r-project.org/web/packages/Platypus
Previous versions and publish date:
3.2.3 (2021-10-19 09:00), 3.3.2 (2022-01-28 00:20), 3.3.5 (2022-04-11 19:42), 3.4.1 (2022-08-15 09:20), 3.5.0 (2024-02-21 21:40)
Other packages that cited Platypus R package
View Platypus citation profile
Other R packages that Platypus depends, imports, suggests or enhances
Functions, R codes and Examples using the Platypus R package
Some associated functions: AbForests_AntibodyForest . AbForests_CompareForests . AbForests_ConvertStructure . AbForests_CsvToDf . AbForests_ForestMetrics . AbForests_PlotGraphs . AbForests_PlyloToMatrix . AbForests_RemoveNets . AbForests_SubRepertoiresByCells . AbForests_SubRepertoiresByUniqueSeq . AbForests_UniqueAntibodyVariants . AlphaFold_prediction . AntibodyForests . AntibodyForests_communities . AntibodyForests_dynamics . AntibodyForests_embeddings . AntibodyForests_expand_intermediates . AntibodyForests_heterogeneous . AntibodyForests_infer_ancestral . AntibodyForests_join_trees . AntibodyForests_kernels . AntibodyForests_label_propagation . AntibodyForests_metrics . AntibodyForests_node_transitions . AntibodyForests_overlap . AntibodyForests_paths . AntibodyForests_phylo . AntibodyForests_plot . AntibodyForests_plot_metrics . Bcell_sequences_example_tree . Bcell_tree_2 . CellPhoneDB_analyse . Echidna_simulate_repertoire . Echidna_vae_generate . GEX_DEgenes . GEX_DEgenes_persample . GEX_GOterm . GEX_GSEA . GEX_clonotype . GEX_cluster_genes . GEX_cluster_genes_heatmap . GEX_cluster_membership . GEX_coexpression_coefficient . GEX_dottile_plot . GEX_gene_visualization . GEX_heatmap . GEX_lineage_trajectories . GEX_pairwise_DEGs . GEX_phenotype . GEX_phenotype_per_clone . GEX_projecTILS . GEX_proportions_barplot . GEX_pseudobulk . GEX_pseudotime_trajectory_plot . GEX_scatter_coexpression . GEX_topN_DE_genes_per_cluster . GEX_trajectories . GEX_visualize_clones . GEX_volcano . PlatypusDB_AIRR_to_VGM . PlatypusDB_VGM_to_AIRR . PlatypusDB_fetch . PlatypusDB_find_CDR3s . PlatypusDB_list_projects . PlatypusDB_load_from_disk . PlatypusML_balance . PlatypusML_classification . PlatypusML_feature_extraction_GEX . PlatypusML_feature_extraction_VDJ . Spatial_VDJ_assignment . Spatial_VDJ_plot . Spatial_celltype_plot . Spatial_cluster . Spatial_density_plot . Spatial_evolution_of_clonotype_plot . Spatial_marker_expression . Spatial_module_expression . Spatial_nb_SHM_compare_to_germline_plot . Spatial_scaling_parameters . Spatial_selection_expanded_clonotypes . Spatial_selection_of_cells_on_image . Spatial_vgm_formation . VDJ_GEX_clonal_lineage_clusters . VDJ_GEX_clonotyme . VDJ_GEX_clonotype_clusters_circos . VDJ_GEX_expansion . VDJ_GEX_integrate . VDJ_GEX_matrix . VDJ_GEX_overlay_clones . VDJ_GEX_stats . VDJ_VJ_usage_circos . VDJ_Vgene_usage . VDJ_Vgene_usage_barplot . VDJ_Vgene_usage_stacked_barplot . VDJ_abundances . VDJ_alpha_beta_Vgene_circos . VDJ_analyze . VDJ_antigen_integrate . VDJ_assemble_for_PnP . VDJ_bulk_to_vgm . VDJ_call_MIXCR . VDJ_call_MIXCR_full . VDJ_call_RECON . VDJ_call_enclone . VDJ_circos . VDJ_clonal_donut . VDJ_clonal_expansion . VDJ_clonal_expansion_abundances . VDJ_clonal_lineages . VDJ_clonotype . VDJ_contigs_to_vgm . VDJ_db_annotate . VDJ_db_load . VDJ_diversity . VDJ_dublets . VDJ_dynamics . VDJ_enclone . VDJ_expand_aberrants . VDJ_extract_germline . VDJ_get_public . VDJ_isotypes_per_clone . VDJ_kmers . VDJ_logoplot_vector . VDJ_network . VDJ_ordination . VDJ_overlap_heatmap . VDJ_per_clone . VDJ_phylogenetic_trees . VDJ_phylogenetic_trees_plot . VDJ_plot_SHM . VDJ_public . VDJ_rarefaction . VDJ_reclonotype_list_arrange . VDJ_select_clonotypes . VDJ_structure_analysis . VDJ_tree . VDJ_variants_per_clone . VGM_expand_featurebarcodes . VGM_expanded_clones . VGM_integrate . automate_GEX . call_MIXCR . class_switch_prob_hum . class_switch_prob_mus . clonofreq.isotype.data . clonofreq.isotype.plot . clonofreq . clonofreq.trans.data . clonofreq.trans.plot . cluster.id.igraph . colors . dot_plot . get.avr.mut.data . get.avr.mut.plot . get.barplot.errorbar . get.elbow . get.n.node.data . get.n.node.plot . get.seq.distance . get.umap . get.vgu.matrix . hotspot_df . hum_b_h . hum_b_l . hum_t_h . hum_t_l . iso_SHM_prob . mus_b_h . mus_b_l . mus_b_trans . mus_t_h . mus_t_l . no.empty.node . one_spot_df . pheno_SHM_prob . select.top.clone . small_vgm . special_v . trans_switch_prob_b . trans_switch_prob_t . umap.top.highlight . vdj_length_prob . 
Some associated R codes: AbForests_AntibodyForest.R . AbForests_CompareForests.R . AbForests_ConvertStructure.R . AbForests_CsvToDf.R . AbForests_ForestMetrics.R . AbForests_PlotGraphs.R . AbForests_PlyloToMatrix.R . AbForests_RemoveNets.R . AbForests_SubRepertoiresByCells.R . AbForests_SubRepertoiresByUniqueSeq.R . AbForests_UniqueAntibodyVariants.R . AbForests_data.R . AbForests_internal.R . AlphaFold_prediction.R . AntibodyForests.R . AntibodyForests_communities.R . AntibodyForests_dynamics.R . AntibodyForests_embeddings.R . AntibodyForests_expand_intermediates.R . AntibodyForests_heterogeneous.R . AntibodyForests_infer_ancestral.R . AntibodyForests_join_trees.R . AntibodyForests_kernels.R . AntibodyForests_label_propagation.R . AntibodyForests_metrics.R . AntibodyForests_node_transitions.R . AntibodyForests_overlap.R . AntibodyForests_paths.R . AntibodyForests_phylo.R . AntibodyForests_plot.R . AntibodyForests_plot_metrics.R . CellPhoneDB_analyse.R . Echidna_Internal_functions.R . Echidna_data.R . Echidna_other_functions.R . Echidna_simulate_repertoire.R . Echidna_vae_generate.R . Echidna_vae_internal_functions.R . GEX_DEgenes.R . GEX_DEgenes_persample.R . GEX_GOterm.R . GEX_GSEA.R . GEX_clonotype.R . GEX_cluster_genes.R . GEX_cluster_genes_heatmap.R . GEX_cluster_membership.R . GEX_coexpression_coefficient.R . GEX_dottile_plot.R . GEX_gene_visualization.R . GEX_heatmap.R . GEX_lineage_trajectories.R . GEX_pairwise_degs.R . GEX_phenotype.R . GEX_phenotype_per_clone.R . GEX_projecTILS.R . GEX_proportions_barplot.R . GEX_pseudobulk.R . GEX_pseudotime_trajectory_plot.R . GEX_scatter_coexpression.R . GEX_topN_DE_genes_per_cluster.R . GEX_trajectories.R . GEX_visualize_clones.R . GEX_volcano.R . PlatypusDB_AIRR_to_VGM.R . PlatypusDB_VGM_to_AIRR.R . PlatypusDB_fetch.R . PlatypusDB_find_CDR3s.R . PlatypusDB_list_projects.R . PlatypusDB_load_from_disk.R . PlatypusML_balance.R . PlatypusML_classification.R . PlatypusML_feature_extraction_GEX.R . PlatypusML_feature_extraction_VDJ.R . Platypus_data.R . Spatial_VDJ_assignment.R . Spatial_VDJ_plot.R . Spatial_celltype_plot.R . Spatial_cluster.R . Spatial_density_plot.R . Spatial_evolution_of_clonotype_plot.R . Spatial_marker_expression.R . Spatial_module_expression.R . Spatial_nb_SHM_compare_to_germline_plot.R . Spatial_scaling_parameters.R . Spatial_selection_expanded_clonotypes.R . Spatial_selection_of_cells_on_image.R . Spatial_vgm_formation.R . VDJ_GEX_clonal_lineage_clusters.R . VDJ_GEX_clonotyme.R . VDJ_GEX_clonotype_clusters_circos.R . VDJ_GEX_expansion.R . VDJ_GEX_integrate.R . VDJ_GEX_matrix.R . VDJ_GEX_overlay_clones.R . VDJ_GEX_stats.R . VDJ_VJ_usage_circos.R . VDJ_Vgene_usage.R . VDJ_Vgene_usage_barplot.R . VDJ_Vgene_usage_stacked_barplot.R . VDJ_abundances.R . VDJ_alpha_beta_Vgene_circos.R . VDJ_analyze.R . VDJ_antigen_integrate.R . VDJ_assemble_for_PnP.R . VDJ_bulk_to_vgm.R . VDJ_call_MIXCR.R . VDJ_call_MIXCR_full.R . VDJ_call_enclone.R . VDJ_call_recon.R . VDJ_circos.R . VDJ_clonal_donut.R . VDJ_clonal_expansion.R . VDJ_clonal_expansion_abundances.R . VDJ_clonal_lineages.R . VDJ_clonotype.R . VDJ_contigs_to_vgm.R . VDJ_db_annotate.R . VDJ_db_load.R . VDJ_diversity.R . VDJ_dublets.R . VDJ_dynamics.R . VDJ_enclone.R . VDJ_expand_aberrants.R . VDJ_extract_germline.R . VDJ_get_public.R . VDJ_isotypes_per_clone.R . VDJ_kmers.R . VDJ_logoplot_vector.R . VDJ_network.R . VDJ_ordination.R . VDJ_overlap_heatmap.R . VDJ_per_clone.R . VDJ_phylogenetic_trees.R . VDJ_phylogenetic_trees_plot.R . VDJ_plot_SHM.R . VDJ_public.R . VDJ_rarefaction.R . VDJ_reclonotype_list_arrange.R . VDJ_select_clonotypes.R . VDJ_structure_analysis.R . VDJ_tree.R . VDJ_variants_per_clone.R . VGM_expand_featurebarcodes.R . VGM_expanded_clones.R . VGM_integrate.R . automate_GEX.R . call_MIXCR.R . dot_plot.R .  Full Platypus package functions and examples
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