Man pages for BgeeDB/BgeeCall
Automatic RNA-Seq present/absent gene expression calls generation
| AbundanceMetadata-class | AbundanceMetadata s4 class |
| BgeeCall | generate gene expression calls with BgeeCall |
| BgeeMetadata-class | BgeeMetadata S4 class |
| create_kallisto_index | Create kallisto indexes. |
| download_fasta_intergenic | Download fasta intergenic |
| download_kallisto | Download binary version of kallisto. |
| generate_calls_workflow | generate present/absent calls |
| generate_presence_absence | Generate presence absence |
| generate_slurm_calls | Generate present/absent calls on slurm queuing system |
| generate_slurm_indexes | Generate all indexes for the abundance quantification step |
| getIntergenicPrefix | 'intergenic_prefix' Getter |
| getIntergenicRelease | 'intergenic_release' Getter |
| getRunIds | 'run_ids' Getter |
| getSimpleArborescence | 'simple_arborescence' Getter |
| get_summary_stats | Gather statistical information |
| getWorkingPath | 'working_path' Getter |
| KallistoMetadata-class | KallistoMetadata S4 class |
| list_bgee_ref_intergenic_species | List species having Bgee reference intergenic sequences |
| list_community_ref_intergenic_species | List species having reference intergenic sequences created by... |
| list_intergenic_release | List reference intergenic releases usable with the BgeeCall... |
| merge_transcriptome_and_intergenic | Merge transcriptome file provided by the user with the Bgee... |
| merging_libraries | Calls of expression in combined libraries |
| run_kallisto | Run one kallisto abundance analyse |
| run_tximport | Run tximport |
| setAnnotationFromFile | Set annotation_object of one UserMetadata object |
| setAnnotationFromObject | Set annotation_object of one UserMetadata object |
| setIntergenicRelease | 'intergenic_release' Setter |
| setOutputDir | 'output_dir' Setter |
| setRNASeqLibPath | 'rnaseq_lib_path' Setter |
| setRunIds | 'run_ids' Setter |
| setSimpleArborescence | 'simple_arborescence' Setter |
| setTranscriptomeFromFile | Set transcriptome_object of one UserMetadata object |
| setTranscriptomeFromObject | Set transcriptome_object of one UserMetadata object |
| setWorkingPath | 'working_path' Setter |
| UserMetadata-class | UserMetadata S4 class |
