Man pages for CharlesJB/rnaseq
Wrapper Functions for RNA-Seq Post-Processing
| batch_de | Produce differential expression analysis in batch |
| batch_pca | Produce PCA in batch |
| batch_volcano | Produce volcano plots in batch |
| create_dummy_txi | Create a dummy txi objects |
| deseq2_analysis | DESeq2 analysis |
| ERCC92 | ERCC92 data description |
| filter_txi | Filter out txi object |
| format_counts | Prepare formated table counts in odysse format. |
| format_de_odysse | Prepare formated DE table in odysse format. |
| format_de_results | Minimal formatting of de results |
| get_anno_df | Extract counts with annotation data.frame from txi |
| get_demo_abundance_files | Get demo kallisto abundance files |
| get_demo_anno_file | Get demo annotation file |
| get_demo_de_infos_file | Get demo de_infos file |
| get_demo_design | Get demo design |
| get_demo_kallisto_dir | Get demo kallisto quant dir |
| get_demo_metadata_file | Get demo metadata file |
| get_demo_pca_infos_file | Get demo pca infos file |
| get_demo_txi | Get demo txi file |
| get_demo_volcano_infos_file | Get demo volcano_infos file |
| get_filenames | Parse kallisto quant directory to retrieve filenames |
| get_human_hsk | Get the list of default human housekeeping genes. |
| get_raw_count_anno_df | Extract raw counts with annotation data.frame from txi |
| get_ruvg_anno_df | Extract RUVg counts with annotation data.frame from txi |
| get_tpm_anno_df | Extract TPM with annotation data.frame from txi |
| import_kallisto | Import quantifications from Kallisto |
| parse_metadata_for_LO_report | Parse metadata LO |
| plot_pca | Produce a PCA plot from produce_pca_df results |
| produce_deliverables | Produce deliverables |
| produce_odysse_format | Save the analysis results in odysse format |
| produce_pca | Deprecated |
| produce_pca_df | Produce a PCA plot from txi |
| produce_report | Produce report in Rmd format |
| produce_RUVSeq_graphs | Produce RUVSeq recommended graph to evaluate normalization |
| produce_volcano | produce a volcano plot from DESeq2 results |
| ruvg_normalization | Normalize data with RUVSeq RUVg algorithm |
| split_de_results | Split differential expression results |
| validate_txi | Validate the txi object content |
| wrapper_report_LO | wrapper report LO |
