Bioconductor release 2.0.0

• Reading chromatograms into memory db.
• Using data.table instead of data.frame for modify-in-place.
• Added support for Metabolomics DIA data.
• Hierarchical clustering based alignment.
• Create a child run (features + chromatograms) from two parents.
• Added support for sqMass files.

Proteomics and Metabolomics alignment

• Added support for metabolomics DIA alignment.
• This is the last release with data.frame based table. From this release onwards, data.table based tables will be used.

data.frame based star and hierarchical alignment

• Hierarchical clustering based alignment.
• Create a child run (features + chromatograms) from two parents.
• Added support for sqMass files.

Fast star-based hybrid alignment

• Supporting transition level intensity for SAINTq
• Added support for pyopenms.
• Added support for sqMass files.
• Added parallelization using BiocParallel.
• Using context-specific qvalues to determine reference.
• Alignment is done over multipeptide instead of multiprecursor.
• Precursors of a peptides are forced to have same feature-RT.
• Savitzky Golay smoothing in C++.
• Fast and light global alignment functions.

Enhancement1

• Function to trim XICs.
• Added filePath, Spectra file name, and RunID in one data frame. No need to pass datapath to each function.
• Separate functions to get precursor IDs, OpenSWATH features and chromatogram indices for each precursor across runs.
• Using multi-peptide and updating it in the parent frame.
• Added Alignment rank column.
• Copied C++ code for peak integration from OpenMS.

Proteomics paper review

• Added as.list function for S4 objects.
• Adde documentation of C++ code: https://shubham1637.github.io/DIAlignR/src/doc/html/index.html