annotSite | Annotate modification site |
BarcodePlotLiP | Barcode plot. Shows protein coverge of LiP modified peptides. |
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. |
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. |
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. |
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. |