Package index
-
ah_shiny() - Interactive table for AnnotationHub
-
fgsea_wrapper()fgsea_go()fgsea_kegg()fgsea_msigdb()fgsea_reactome()fgsea_keywords()fgsea_phenotype()fgsea_disease() - GSEA using fgsea
-
gs_map_to_orthologues() - Generate gene sets by mapping to orthologues
-
gene_level_log2fc()gene_level_s2n()gene_level_tvalue()gene_level_sam()gene_level_log_p()set_level_mean()set_level_median()set_level_maxmean()set_level_wilcox()set_chi_square()set_level_ks() - GSEA framework
-
gsea_plot() - GSEA plot
-
map_to_entrez()guess_id_type()convert_to_entrez() - ID mapping
-
interactive_local() - A REPL in a local environment
-
jaccard()genesets_similarity_heatmap() - Jaccard coefficent
-
list_to_data_frame()data_frame_to_list() - Convert gene sets between list and a data frame
-
load_go_genesets()load_kegg_genesets()load_msigdb_genesets()load_reactome_genesets()load_simona_genesets() - Load various gene sets
-
list_msigdb_versions()list_msigdb_collections()choose_msigdb_collection()get_msigdb() - Retrieve gene sets from MSigDB
-
gsea_sample_perm()gsea_gene_perm() - Native implementation of GSEA
-
ora()ora_go()ora_kegg()ora_msigdb()ora_reactome()ora_keywords()ora_phenotype()ora_disease() - Over-representation analysis
-
get_GO_gene_sets_from_orgdb()random_genes()protein_coding_genes() - Get genes and GO terms from OrgDb oject
-
p53_dataset - P53 dataset
-
seqlengths_as_GRanges() - Create a GRanges object from seqlengths
-
ss_gsea() - Single-sample GSEA transformation
-
retrieve_all_kegg_graphs()ora_kegg_topology()gsea_kegg_topology() - Centrality-based KEGG enrichment analysis
-
wrap_text() - Wrap long text into multiple lines