NEWS
DIAlignR 2.1.4
- 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.
DIAlignR 2.1.0
- 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.
DIAlignR 1.3.18
- 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.
DIAlignR 1.3.5
- 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.
DIAlignR 1.1.5
- ananlyteFDR to limit features for multipeptide.
- Removed decoy from features.
- BugFix alignment if all intensities are zero.
- Fixed printed stats.
DIAlignR 0.99.26
- Fixed visualization function.
- Calculating global alignment before iterating over multipeptides.
- Added summary after the alignment.
- Fixed area integrator for missing boundaries.
DIAlignR 0.99.25
- 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.
DIAlignR 0.99.13
- Added as.list for S4 objects
DIAlignR 0.99.12
- 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
DIAlignR 0.99.11
- Made changes as suggested in initial review. Updated man/ pages associated with function.
- Link to the file for generating example data is updated.
DIAlignR 0.99.10
- Made changes as suggested in initial review. https://github.com/Bioconductor/Contributions/issues/1328#issuecomment-576806498
DIAlignR 0.99.9
- Added option to include mz pointer in getOswFiles and getXIC4AlignObj
DIAlignR 0.99.8
- Removed R version dependency, have rda files instead of Rdata
DIAlignR 0.99.7
- Lowered R version dependency
DIAlignR 0.99.4
- Upadted version number
- Corrected tests
- Updated tests to reflect mzR updates, included travis-CI build
- Moved package to Bioconductor