annotSite | Annotate modification site |
calculateProteolyticResistance | Calcutates proteolytic resistance for provided data. Requires input from dataSummarizationLiP function. Can optionally calculate differential analysis using proteolytic resistance. In order for this function to work, Conditions and run numbers must match between the LiP and TrP data. |
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 MSstats. |
DIANNtoMSstatsLiPFormat | Converts raw LiP MS data from DIA-NN into the format needed for MSstatsLiP. |
groupComparisonLiP | Model LiP and TrP data and make adjustments if needed Returns list of three modeled datasets |
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 in protein structures caused by compound binding in cellur lysates. |
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 score of different fully tryptic peptides in a protein. |
SkylineTest | SkylineTest |
SkylinetoMSstatsLiPFormat | Converts raw LiP MS data from Skyline into the format needed for MSstatsLiP. |
SpectronauttoMSstatsLiPFormat | Converts raw LiP MS data from Spectronautt into the format needed for MSstatsLiP. |
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 proteotypicity, and then uses calcualtions in histogram. |