Man pages for Vitek-Lab/MSstatsLiP
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
| annotSite | Annotate modification site |
| calculateProteolyticResistance | Calcutates proteolytic resistance for provided data. Requires... |
| calculateTrypticity | Calculates level of trypticity for a list of LiP Peptides. |
| correlationPlotLiP | Plot run correlation for provided LiP and TrP experiment. |
| dataProcessPlotsLiP | Visualization for explanatory data analysis |
| dataSummarizationLiP | Summarizes LiP and TrP datasets seperately using methods from... |
| DIANNtoMSstatsLiPFormat | Converts raw LiP MS data from DIA-NN into the format needed... |
| groupComparisonLiP | Model LiP and TrP data and make adjustments if needed Returns... |
| groupComparisonPlotsLiP | Visualization for model-based analysis and summarization |
| LiPRawData | LiPRawData |
| locateMod | Locate modified sites with a peptide |
| locatePTM | Annotate modified sites with associated peptides |
| MSstatsLiP | MSstatsLiP: A package for identifying and analyzing changes... |
| MSstatsLiP_data | MSstatsLiP_data |
| MSstatsLiP_model | MSstatsLiP_model |
| MSstatsLiP_Summarized | MSstatsLiP_Summarized |
| PCAPlotLiP | Visualize PCA analysis for LiP and TrP datasets. |
| raw_lip | raw_lip |
| raw_prot | raw_prot |
| ResistanceBarcodePlotLiP | Proteolytic Resistance Barcode plot. Shows accessibility... |
| SkylineTest | SkylineTest |
| SkylinetoMSstatsLiPFormat | Converts raw LiP MS data from Skyline into the format needed... |
| SpectronauttoMSstatsLiPFormat | Converts raw LiP MS data from Spectronautt into the format... |
| StructuralBarcodePlotLiP | Barcode plot. Shows protein coverge of LiP modified peptides. |
| tidyFasta | Read and tidy a FASTA file |
| TrPRawData | TrPRawData |
| trypticHistogramLiP | Histogram of Half vs Fully tryptic peptides. Calculates... |
