- BioTransition::ppi_hHuman Protein-Protein Interaction Network
- BioTransition::ppi_mMouse Protein-Protein Interaction Network
- Connectome::ncomms8866FANTOM5 Ligand-Receptor Database (Original)
- Connectome::ncomms8866_humanFANTOM5 Ligand-Receptor Database (Human)
- Connectome::ncomms8866_mouseFANTOM5 Ligand-Receptor Database (Mouse)
- Connectome::ncomms8866_pigFANTOM5 Ligand-Receptor Database (Pig)
- Connectome::ncomms8866_ratFANTOM5 Ligand-Receptor Database (Rat)
- Connectome::translatorGene Symbol Translator
- fastCNV::geneMetadataGenes Data from Ensembl Version 113
- hdWGCNA::test_seurat
- iTALK::databaseLigand-Receptor Interaction Database
- MAGICR::magic_testdataExample Single-Cell Data for MAGICR
- METAFLUX::bulk_test_exampleBulk test example
- METAFLUX::cell_mediumThis file contains the hams medium nutrients information
- METAFLUX::human_bloodThis file contains the hams medium nutrients information in human blood
- METAFLUX::human_gemHuman-GEM Metabolic Model Data
- METAFLUX::nutrient_lookup_files1648 exchange reactions:mathematical representation of uptake/secrete metabolites into the extracellular space
- METAFLUX::sc_test_examplesingle cell test seurat object example
- MOFSR::gene_setsFunctional Gene Sets
- MultiK::p3clThree Cell Line Mixture Dataset
- multinichenetr::geneinfo_alias_humanGene annotation information: version 2 - january 2022 - suited for alias conversion
- multinichenetr::geneinfo_alias_mouseGene annotation information: version 2 - january 2022 - suited for alias conversion
- multinichenetr::ligand_target_matrix_testLigand-Target Matrix: subset NicheNet 2.0.
- multinichenetr::sceSingleCellExperiment object containing scRNAseq data (subsampled)
- nichenetr::annotation_data_sourcesAnnotation table of all data sources used in the NicheNet model
- nichenetr::expression_settings_validationExpression datasets for validation
- nichenetr::geneinfo_2022Gene annotation information: version 2 - january 2022
- nichenetr::geneinfo_alias_humanGene annotation information: version 2 - january 2022 - suited for alias conversion
- nichenetr::geneinfo_alias_mouseGene annotation information: version 2 - january 2022 - suited for alias conversion
- nichenetr::geneinfo_humanGene annotation information
- nichenetr::hyperparameter_listOptimized hyperparameter values
- nichenetr::ncitationsNumber of citations for genes
- nichenetr::optimized_source_weights_dfOptimized data source weights
- nichenetr::source_weights_dfData source weights
- SCENT::net13Jun12.mProtein-Protein Interaction Network
- scFOCAL::L1000_compoundsL1000_compounds
- scFOCAL::L1000_genesL1000_genes
- scFOCAL::LINCS.ResponseSigsLINCS.ResponseSigs
- scGate::genes.blacklist.defaultBlocklist of genes for dimensionality reduction
- scGate::query.seuratToy dataset to test the package
- scMetaLink::crc_exprCRC Example Expression Data
- scMetaLink::crc_metaCRC Example Cell Metadata
- scMetaLink::metalinksdbMetalinksDB Database
- scMetaLink::st_exprColon Spatial Transcriptomics Expression Data
- scMetaLink::st_metaColon Spatial Transcriptomics Metadata
- scMetaLink::st_scalefactorsColon Spatial Transcriptomics Scale Factors
- SCORPION::scorpionTestExample single-cell gene expression, motif, and ppi data
- scPharm::bulkdataBulk RNA-seq Expression Data for Cancer Cell Lines
- scPharm::copykat_cyclegenesCell Cycle Genes for CNV Analysis
- scPharm::copykat_DNA.hg20Genomic Bin Coordinates for hg38
- scPharm::copykat_full.anno.hg20Human Gene Annotations for hg38
- scPharm::drug_infoGDSC2 Drug Information
- scPharm::gdscdataGDSC2 Pharmacogenomics Data
- SpaTalk::geneinfogeneinfo
- SpaTalk::lrpairslrpairs
- SpaTalk::pathwayspathways
- SVG::example_svg_dataExample Spatial Transcriptomics Data
- tradeSeq::celltypeA vector defining cell types, used in the package vignette.
- tradeSeq::countMatrixA count matrix, used in the package vignette.
- tradeSeq::crvA SlingshotDataset object, used in the package vignette.
- tradeSeq::gamListA list of GAM models, used to demonstrate the various tests.
- tradeSeq::sdsA SlingshotDataset object, used in the package unit tests.
- yaGST::rankedListAn example of pre-ranked list.
