Man pages for RGLab/HIPCMatrix
Microarray and RNA-seq Processing for ImmuneSpace
| chaussabel_modules | Modules from Chaussabel (2008) |
| create_gene_alias_map | Create Gene Alias Map |
| dot-fix_headers | fix headers |
| dot-ge_list_to_flat_file | matrix list to flat file |
| dot-getGEO_custom | getGEO (custom) |
| dot-get_geo_supp_files | Get GEO supp files |
| dot-get_supp_files_dir | Get supplemental files directory |
| dot-make_id_to_gsm_map | Make id to GSM map |
| dot-map_feature_id_col | Standardize probe column name |
| dot-map_sampleid_to_biosample_accession | Map experiment-sample or geo accessions to biosample... |
| dot-prep_geo_files | Prep GEO files |
| dot-prep_illumina_headers | Prep Illumina Headers |
| dot-prep_immport_files | Prep ImmPort Files |
| dot-process_affy | Process Affy |
| dot-process_illumina | Process Illumina |
| dot-process_rna_seq | Process RNA-seq |
| dot-process_two_color_array | Process Two Color Array |
| dot-select_input_files | Select input files |
| dot-subset_raw_illumina_dt | Subset Illumina raw data |
| dot-write_raw_expression | Write raw expression to a file |
| emory_blood_transcript_modules | Blood transcriptome modules |
| find_de_genes_eBayes | Find Differentially Expressed genes using Empirical Bayes... |
| format_predictor_table | Format Predictor Table |
| get_meta_data | Get Meta Data |
| gsea | Gene Set Enrichment Analysis |
| hgncAlias2Symbol | data.table mapping gene aliases to gene symbols |
| hgncAlias2Symbol_version | Date hgncAlias2Symbol update |
| HMX | HIPCMatrix Connection |
| makeAnnoDf | make annotation df |
| make_raw_matrix | Make Raw Matrix |
| mapAlias2Symbol | map alias to gene symbol |
| meta_data_list | List of study-specific metadata |
| msigdb_immunologic_signatures | Immunologic signatures |
| normalize_matrix | Normalize matrix |
| normalize_microarray | Normalize microarray data |
| normalize_rnaseq | Normalize raw RNA-seq data |
| orig_btm_list | Original HIPC BTM list |
| orig_chaussabel | Modules from Chaussabel (2008) |
| orig_emory | Blood transcriptome modules |
| orig_msigdb | Immunologic signatures |
| print.ImmuneResponsePredictor | Print an ImmuneResponsePredictor object |
| retrieve_input_files | Retrieve input files |
| runCreateMx | Run Create Matrix |
| summarize_by_gene_symbol | Summarize Matrix |
| updated_btm_df | Updated HIPC BTM data frame |
| updated_btm_list | Updated HIPC BTM list |
| update_geneset_symbols | Update Geneset Symbols |
| write_matrix | Write matrix to file system |
