Man pages for alexvpickering/rkal
Run, Import, and Export 'kallisto' Quantifications
| build_kallisto_index | Download ensembl transcriptome and build index for 'kalliso'... |
| construct_eset | Construct expression set |
| detect_paired | Detect if experiment is pair-ended. |
| filter_genes | Filter genes in RNA-seq ExpressionSet |
| get_fastq_id1s | Get first sequence identifiers for fastq.gz files |
| get_fastq_pairs | Get pairs from bulk fastq files |
| get_kallisto_index | Get path to kallisto index |
| get_pkg_version | Get version of kallisto from system command. |
| get_quant_meta | Transform GEO metadata for quantification |
| get_vsd | Get variance stabilized data for exploratory data analysis |
| import_quants | Import kallisto quants |
| load_archs4_seq | Load ExpressionSet from ARCHS4 h5 file |
| load_seq | Load bulk RNA-Seq data into an ExpressionSet. |
| run_kallisto_bulk | Runs kallisto quantification for bulk samples. |
| select_pairs | Select pairs and replicates for an experiment. |
| setup_fdata | Setup feature annotation data |
| validate_pairs | Validate sample pairing for pair-ended RNA seq |
| validate_reps | Validate sample replicates for RNA seq |
