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:
Platypus_3.6.0.tar.gz
Platypus_3.6.0.tar.gz(r-4.5-noble)Platypus_3.6.0.tar.gz(r-4.4-noble)
Platypus_3.6.0.tgz(r-4.4-emscripten)Platypus_3.6.0.tgz(r-4.3-emscripten)
Platypus.pdf |Platypus.html✨
Platypus/json (API)
NEWS
# Install 'Platypus' in R: |
install.packages('Platypus', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:9d71944457. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 18 2024 |
R-4.5-linux | OK | Dec 18 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