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pmd 0.2.7

• CRAN
• Change URL to doi for citation
• remove dependance of msnbase, function pmdanno has been moved to rmwf package

pmd 0.2.6

• Add getpmddf to show pmd details with given m/z only data and m/z group information(optional, segmentation m/z group for spatial reactomics analysis)
• Update reactomics vignette with section “Reactomics analysis for MS only data” and showcase the quantitative analysis for certain PMD
• add support for mass only data for getchain

pmd 0.2.5

• Add KEGG reaction class and enzyme number to the keggrall database
• Fix url of demo data

pmd 0.2.4

• add support for mass only data for quantitative reactomics analysis
• add quantitative methods for dynamic pmds
• add support for multiple pmds in getpmd function
• update reactomics vignette to add more details for quantitative analysis of PMD
• update getchain to handle large data
• add mass defect filter for getrda and getpaired to retain reaction related PMDs
• add parameter for getrda for pmd sets and mass defect table
• change getchain corcutoff to 0.6

pmd 0.2.3

• add MaConDa database
• fix NULL default value issue in shiny apps

pmd 0.2.2

• spell check
• goodpractice package check

pmd 0.2.1

• CRAN

pmd 0.2.0

• add option to skip sda in GlobalStd algorithm and set default to F
• organize the R files
• add vignette for reactomics analysis
• add correlation directed analysis function
• modified getcorcluster function to find independent peaks
• add vignette section for reduced independent peaks selection in GlobalStd algorithm
• fix the issue for getchain with multiple masses
• fix the correlation issue in pos/neg linkage function
• Output within RT clusters high frequencies PMD(s) as message for user to check
• Change default ng to NULL in getpared function for automated generate parameter based on data
• update with citation of cc paper
• fix the bug in pmd ms/ms annotation due to the change of enviGCMS package
• fix the order issue from CRAN

pmd 0.1.9

• CRAN

pmd 0.1.8

• update kegg/hmdb database
• update getsda to use largest average distance to find pmd frequency cutoff, more robust to large dataset

pmd 0.1.7

• add function for pmd ms/ms annotation
• add function to read in msp file as database
• detach rcdk package
• add function to link pos/neg by pmd

pmd 0.1.6

• rewrite getchain to speed up
• add shiny application pmdnet to perform PMD network analysis
• add support for formula in getchain to find compounds ions
• remove frequency cutoff in getsda and use PMD network clusters analysis to determine the cutoff
• add merge feature for getcluster and such methods could be used to further reduce the GlobalStd peaks
• remove hmdbp data since pmd network analysis could cover this topic
• remove the dependence of group for quantitative paired peaks
• improve shiny application for sda analysis

pmd 0.1.5

• CRAN

pmd 0.1.4

• isotope selection improved to get rid of 1&2 issue
• fix top issue in getsda
• fix peak index issue in getcluster
• add corcutoff for getpmd

pmd 0.1.3

• speed up GlobalStd by mapply
• add message for getrda
• add hmdb pmd analysis results as dataset
• add digits for mass accuracy
• fix the ms1 larger issue in getpmd
• add correlations in getpmd
• add support for quantitative paired peaks list selection for specific reaction
• add support for target pmd and compound analysis for reaction chain

pmd 0.1.2

• update vignettes
• change default ng value into auto-detection
• add top option to limit sda output
• add support for GlobalStd based targeted analysis
• add support to extract specific pmd across different retention time groups
• add PCA similarity factor function from EvolQG package
• add support to export std peaks based on correlation within retention time group
• add support to export index for peaks with highest intensity in peaks cluster
• add support to use intensity data to refine GlobalStd results
• add support to generate sda analysis for mass list only #5
• remove multi chargers with a strict rule #4
• add parameter selection part in vignette #3
• add support for peaks cluster output #2
• add support for formula generation in enviGCMS package #1

pmd 0.1.1

• CRAN with ACA publication

pmd 0.1.0

• new package for paired mass distance analysis

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.