API Overview

Importing Software Results and FASTA Files

The reader and fasta modules allow integrating external data into msreport workflows. The fasta module enables import of protein sequence databases from FASTA files into protein databases. The reader module handles the parsing and standardization of quantitative proteomics output from various software packages, and annotation with FASTA-related metadata, such as information from FASTA headers.

High-Level Data Interface

The qtable, analyze, plot, and export modules form the high-level interface for working with quantitative proteomics data in msreport. The qtable module defines the central Qtable data structure itself. Building upon this, the analyze module offers post-processing and statistical analysis capabilities. For tasks like normalization and imputation, it provides functions that can utilize a variety of transformer classes available from other msreport modules. The plot module enables data visualization, and the export module provides data conversion to various external formats. By directly operating on Qtable instances, these high-level modules provide a straightforward and effective way for analyzing quantitative proteomics data.

Data Transformation Classes

The impute, normalize, and isobar modules provide a collection of transformer classes for processing quantitative proteomics data like imputation or normalization. These transformers follow a consistent "fit-and-transform" pattern, they can be fitted to a training table to learn specific parameters, and then be applied to other tables to perform the transformation.

Auxiliary Modules

These modules provide supplementary functionalities that support various stages of proteomics data processing. The aggregate module offers comprehensive tools for summarizing and reshaping tabular data, including specialized algorithms like MaxLFQ. The peptidoform module defines the core Peptide class for robust representation and manipulation of peptide sequences and modifications. Finally, the helper module provides various utility and helper functions.

Overview of available modules

Module	Description
aggregate	A comprehensive set of tools for aggregating and reshaping tabular proteomics data.
analyze	Tools for post-processing and statistical analysis of Qtable data.
export	Exporting of proteomics data from Qtable into external formats.
fasta	Functionalities for import and access to protein sequence databases from FASTA files.
helper	A collection of widely used helper and utility functions.
impute	Transformer classes for imputing missing values in quantitative proteomics data.
isobar	Provides a transformer class for processing isobarically labeled proteomics data.
normalize	Transformer classes for normalizing and transforming quantitative proteomics data.
peptidoform	Defines the Peptide class and associated utilities for handling peptidoforms.
plot	Plotting functions for visualizing proteomics data from Qtable.
qtable	Defines the Qtable class, the central container for quantitative proteomics data.
reader	Provides tools for importing and standardizing quantitative proteomics data.