Man pages for brucemoran/RNAseqR
RNAseq DE Analysis Downstream from Nextflow Pipelines
| biomaRt_anno_orth | Take two inputs of datasets in biomaRt::useMart and return... |
| BMplotPCA | Plotting PCA function |
| brucemoran_rnaseq_kallisto_parser | Take metadata CSV, parse Kallisto output and return a Sleuth... |
| DESeq2_module | DESeq2 module taking metadata_csv nad raw count data frame to... |
| dupradar_run | Function to run fGSEA using the mSIGDB database from Broad |
| edgeR_module | edgeR module taking metadata_csv and raw count data frame to... |
| fgsea_plot | Function to run fGSEA using the mSIGDB database from Broad |
| fgsea_ssgsea_msviper | Run fgsea on each regulon set individually |
| found_in_three | Found-in-3 |
| found_in_two | Found-in-2 |
| genesGTF | Parse information from STAR run to find used GTF file |
| get_metadata | Make metadata from CSV input, including generation of 'path'... |
| get_tx2gene | Get annotation in tx2gene format; returns hsapiens_homolog... |
| group_agg_multi | Aggregate columns 3, 4 based on grouping on columns 1, 2 NB... |
| group_agg_two | Aggregate column 1 based on grouping by column 2 |
| highest_exp_wides | The situation arises where a single gene name maps to... |
| limma_module | Limma module taking metadata_csv and raw count data frame to... |
| make_aracne_inputs | Make required inputs for ARACNe-AP which is now supported... |
| master_parse_join | Master list, join to give found-in-2 and all-3 tables |
| msigdb_pathways_to_list | msigdb pathways in a nice list |
| nf_core_rnaseq_featco_parser | Parse featurecounts input as a follow-on from standard... |
| nf_core_rnaseq_star_salmon_parser | Parse featurecounts input as a follow-on from standard... |
| obs_raw_widen | Create wide tibble from sleuth object sums transcripts from a... |
| parse_aracne | Parse inputs (from aracne-ap_viper Nextflow) |
| per_contrast_fgsea_de | Function to take output table from multiple contrasts take... |
| run_msviper | Run msViper |
| run_prep_modules_bm | Wrap prep and module for data from brucemoran RNAseq_kallisto... |
| so_obs_raw_out | Add wide and long raw count tibbles to sleuth object sums... |
| so_to_raw_counts | so to raw_counts_df |
| ssgsea_pca | Function to run ssGSEA using the GSVA package and return PCA... |
| ssgsea_rotationPCA | Plotting PCA function |
| stringTie_res_join | Get StringTie TPM results |
| venn_3 | Make venn diagram |
