Man pages for greenelab/ADAGEpath
ADAGE-based Signature Analysis
| ADAGEpath | ADAGEpath: ADAGE-based Signature Analysis |
| annotate_genes_in_signatures | Annotating genes in signatures |
| annotate_shared_signatures | Shared signature annotation |
| annotate_signatures_with_genesets | Signatures annotation with gene sets |
| build_gene_geneset_map | Gene-geneset map |
| build_limma | Building a linear regression model for differential analysis |
| build_signature_overlap_matrix | Signature overlap matrix construction |
| calculate_activity | Signature activity calculation |
| calculate_marginal_activity | Marginal activity calculation |
| check_accession | Accession number validity check |
| check_input | Checking input format |
| combine_geneset_outputs | Combining geneset outputs |
| download_raw | Downloading raw data from ArrayExpress |
| eADAGEmodel | eADAGE model |
| enrich_test | Gene set enrichment test |
| experimentID | Experiments and samples in Pseudomonas aeruginosa gene... |
| extract_signatures | Signature extraction |
| fetch_geneset | Gene set fetch |
| find_associated_signatures | Associated signatures retrieval |
| geneinfo | Gene information |
| get_active_signatures | Most active signature retrieval |
| get_paretofront | Pareto fronts calculation |
| get_sample_info | Querying sample information from ArrayExpress |
| impute_miss_values | Missing values imputation |
| load_dataset | Loading and processing input data |
| map_value_to_color | Mapping value to HEX color |
| match_IDs | Matching Gene IDs |
| one_signature | One signature extraction |
| one_signature_activity | One signature activity |
| operons | Pseudomonas aeruginosa PAO1 operons |
| PAcompendium | Pseudomonas aeruginosa gene expression compendium |
| PAO1orthologs | Pseudomonas aeruginosa PAO1 strain orthologs |
| plot_activity_heatmap | Signature activity heatmap |
| plot_marginal_activation | Marginal activation plot |
| plot_signature_overlap | Signature overlap plot |
| plot_volcano | Signature volcano plot |
| prepare_marginal_matrix | Marginal significance matrix preparation |
| probedistribution | Probe distribution |
| process_celfiles | Processing CEL files |
| quantile_norm | Quantile normalization |
| remove_redundant_signatures | Redundant signature removal |
| signature_geneset_activity | Calculating gene set activity inside signatures |
| TDM_RNAseq | RNAseq data normalization with TDM |
| test_signature_overlap | Signature overlap test |
| to_LocusTag | Converting gene ID to locus tag |
| to_symbol | Converting locus tag to symbol |
| visualize_gene_network | Gene-gene network visualization |
| zeroone_norm | Zero-one normalization |
