.tl

The proteopy.tl module provides analysis tools including differential abundance testing, proteoform inference via the COPF algorithm, and clustering methods.

Differential Analysis

proteopy.tl.differential_abundance

Perform differential abundance analysis between sample groups.

Clustering

proteopy.tl.hclustv_tree	Perform hierarchical clustering on variables (peptides or proteins).
proteopy.tl.hclustv_cluster_ann	Annotate variables with cluster assignments from hierarchical clustering.
proteopy.tl.hclustv_profiles	Compute cluster profiles from cluster annotations.

Proteoform Inference (COPF)

The COPF (COrrelation based functional ProteoForm assessment) algorithm enables detection of functional proteoform groups from peptide-level quantitative data [Bludau et al., 2021].

proteopy.tl.pairwise_peptide_correlations
proteopy.tl.peptide_dendograms_by_correlation
proteopy.tl.peptide_clusters_from_dendograms
proteopy.tl.proteoform_scores