CHANGES IN VERSION 2.1.4 (October 19, 2021) ------------------------ + Using non-linear fit to constrain similarity matrix. + Recalculate intensity for given peaks. + Direct alignment to root is added. + Multiple strategies for getting distance matrix and tree-agglomeration is added. + Remove peaks if not aligned. CHANGES IN VERSION 2.1.0 (July 10, 2021) ------------------------ + Added support for IPF based Post-translation Modification alignment. + Added Minimum Spanning Tree based alignment for reference-free approach. + Reintegrate area under the peak for low-confidence peaks. + Supporting Savitzky-Golay smoothing while calculating area. + Added input to select peptides which to align. + Speed improvement in progressive alignment by storing new featues in lists instead of data frames. CHANGES IN VERSION 1.3.18 (February 21, 2021) ------------------------ + 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. CHANGES IN VERSION 1.3.5 (January 03, 2021) ------------------------ + 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. CHANGES IN VERSION 1.1.5 (May 07, 2020) ------------------------ + ananlyteFDR to limit features for multipeptide. + Removed decoy from features. + BugFix alignment if all intensities are zero. + Fixed printed stats. CHANGES IN VERSION 0.99.26 (April 21, 2020) ------------------------ + Fixed visualization function. + Calculating global alignment before iterating over multipeptides. + Added summary after the alignment. + Fixed area integrator for missing boundaries. CHANGES IN VERSION 0.99.25 (April 19, 2020) ------------------------ + 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. CHANGES IN VERSION 0.99.13 (March 31, 2020) ------------------------ + Added as.list for S4 objects CHANGES IN VERSION 0.99.12 (March 02, 2020) ------------------------ + Added boxcar, Gaussian kernel and loess for chromatogram smoothing + Started documentation for C++ code + Added support for Microsoft Visual Studio compiler + Using lists instead of matrix while updating RT and intensities + Moved python code out of the src directory CHANGES IN VERSION 0.99.11 (February 04, 2020) ------------------------ + Made changes as suggested in initial review. Updated man/ pages associated with function. + Link to the file for generating example data is updated. CHANGES IN VERSION 0.99.10 (January 22, 2020) ------------------------ + Made changes as suggested in initial review. https://github.com/Bioconductor/Contributions/issues/1328#issuecomment-576806498 CHANGES IN VERSION 0.99.9 ------------------------ + Added option to include mz pointer in getOswFiles and getXIC4AlignObj CHANGES IN VERSION 0.99.8 ------------------------ + Removed R version dependency, have rda files instead of Rdata CHANGES IN VERSION 0.99.7 ------------------------ + Lowered R version dependency CHANGES IN VERSION 0.99.4 ------------------------ + Upadted version number + Corrected tests + Updated tests to reflect mzR updates, included travis-CI build + Moved package to Bioconductor