Man pages for MassDynamics/lfq_processing
Processes Proteomics Files for Quantification.
| assembleComparisonConditionMapping | This is called in Limma to create a mapping for comparison... |
| decodeComparisonConditionMapping | This function orchestrates the conversion of encoded strings... |
| des_tmt_PXD019880 | TMT Data processed with MaxQuant |
| detect_exp_type | Detect Experiment Type |
| example_lfq_her2_targetted_therapy_tables | HER2 Targetted Therapy processed MaxQuant Data |
| getDownCondition | This function uses the condition comparison mapping to get... |
| get_names_qc_lfq_all | MaxQuant LFQ full QC plots names |
| get_names_qc_lfq_protein_only | MaxQuant FQ protein-only QC plots names |
| get_names_qc_tmt_protein_only | MaxQuant TMT protein-only QC plots names |
| getOriginalFromSafe | This function is a decoder utility that uses the conditions... |
| get_protein_viz | Print a Protein Visualization JSON file. |
| getUpCondition | This function uses the condition comparison mapping to get... |
| impute_lfq | impute LFQ data |
| lfq_quant_analysis | Run Pairwise Protein Quantification on a level of LFQ... |
| lfq_transformer | Run Pairwise Protein Quantification on each level of LFQ... |
| limma_stats_fun | This function performs the differential expression analysis... |
| oneProteinReplData | Transform data for one protein from a long format to the... |
| phospho_enrichment_quant | Run Phosphosite Quantification on each level of Maxquant... |
| protein_groups_tmt_PXD019880 | TMT Data processed with MaxQuant |
| protein_quant_runner | Run Pairwise Protein Quantification and Quality Control on... |
| render_separate_qcs | Render separate QC reports |
| tmt_transformer | Run Pairwise Protein Quantification on each level of TMT... |
| write_output | Write Output of quantitative analysis |
| writeReplicateData | Write Protein counts and intensities json |
