The ReportAnalysis pipeline facilitates statistical analysis and quantitative data exploration for the outputs generated by iSanXoT. It consists of four modules: NMpyCompare, ReportLimma, FDRoptimizer, and qTableReport. Each module is implemented as a Python or R script and is executed using a configuration file.
Download the ReportAnalysis-vx.xx.zip from the last release and unzip the file. Ensure that Python is installed on your system along with the required dependencies. The specific dependencies are detailed in the requirements.txt file.
Description: This Python script calculates NM-corrected values from the iSanXoT report. It subtracts the Zpgm2p value of the associated non-modified peptidoform from the Zpgm2p value of each modified peptidoform. Users can specify column names for integration levels, quantitative values, and criteria for identifying non-modified peptidoforms through the configuration file. The NM-corrected values are then appended as new columns in the iSanXoT report.
Description: This script performs hypothesis testing for comparisons between different groups across integration levels using the limma package. It computes p-values for statistical contrasts, the mean difference between groups, and the LPS value (-log(p-value) adjusted by the sign of the mean difference).
Description: Implemented in Python, this script applies an iterative algorithm to optimize the spectral count threshold at each integration step. It scans different thresholds to maximize the number of elements with a q-value below a user-defined threshold, using the Benjamini-Hochberg algorithm for multiple testing correction.
Description: PTMap is a tool developed with the aim of visualizing, interpreting, and comparing the proteins PTMs of s. This module represents, as many maps as proteins for which any integration meets the threshold established by the user. Each map illustrates the change between one condition and another based on the p-value of all calculated integrations, on the y-axis.
Description: This Python script enables a detailed exploration of significant changes at the protein level in a peptide-centric workflow. It generates an output table summarizing the number of modified and non-modified peptidoforms with significant increases or decreases, along with details on digestion status and qc clusters.
For additional examples and tests, please consult the Test Guide.
For questions or issues, please open an issue on the GitHub repository.