#36 · Tools & infrastructure

Software tools for batch correction, cfDNA fragment analysis and proteomics QC

The dominant thread is software for preprocessing, quality control and normalization of mass spectrometry and cell-free DNA data before biological interpretation. DNAvi provides grouped analysis, normalization, statistical comparison and visualization of cfDNA fragment size profiles. ProteoGyver offers routine QC and analysis of MS-based proteomics data, distributed via GitHub. The preprint is a methods evaluation rather than a distributed tool: it benchmarks seven batch correction methods, including ComBat, Harmony, CCA, FastMNN, scVI, scANVI and Scanorama, for large-scale MALDI mass spectrometry imaging. The shared thread is therefore purpose more than form. What is new is the emphasis on standardized, reusable workflows at the analysis-entry stage, with cross-batch harmonization of imaging data assessed alongside routine proteomics and fragment-level QC. The items do not report adoption metrics, so practical uptake remains undocumented.