Man pages for szymczak-lab/harmonizeGeneExprData
Harmonization of gene expression data from GEO and ArrayExpress
| calculate_time_since_baseline | Calculate time since baseline |
| check_annotation_package | Extract BrainArray annotation package from CEL file |
| check_subject_info | Check subject level information |
| convert_numeric_variable | Convert variable to numeric |
| convert_time_variable | Convert variable to time in days |
| define_batches | Define batches based on scan date |
| download_cel_file | Download CEL file (Affy) from ArrayExpress or GEO |
| download_cel_file_AE | Download CEL file (Affy) from ArrayExpress |
| download_cel_file_GEO | Download CEL file (Affy) from GEO |
| download_files_AE | Download files from ArrayExpress |
| extract_identifier | Extract sample and subject identifiers |
| extract_info_from_idf | Extract information from IDF |
| extract_meta_data | Extract meta data |
| extract_meta_data_AE | Extract meta data from ArrayExpress |
| extract_meta_data_GEO | Extract meta data from GEO |
| extract_pheno_data | Extract phenotype data |
| extract_pheno_data_AE | Extract phenotype data from ArrayExpress |
| extract_pheno_data_GEO | Extract phenotype data from GEO |
| extract_scan_date | Extract scan date |
| extract_subject_id | Extract part of subject identifiers |
| get_expr_data_affy | Download and normalize raw array data |
| harmonize_pheno_data | Harmonize phenotype data |
| make_se_object | Make SummarizedExperiment object |
| map_variable | Harmonize values of a character variable |
| prepare_array_data | Prepare array data |
| prepare_count_data | Prepare count data |
| SRR_2_GSM | Convert SRR identifiers to GSM identifiers (GEO) |
| wrapper_getGEO | Wrapper of the GEOquery::getGEO() function |
