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NEWS.md

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enviGCMS 0.8.0

  • remove the dependency of xcms package

enviGCMS 0.7.4

  • CRAN
  • remove rdisop related example
  • update citation
  • remove dependency of xcms and msnbase
  • add onAttach message for bioc packages

enviGCMS 0.7.3

  • fix getalign2 to accept mz vector without ordering
  • fix getalign ppm bug

enviGCMS 0.7.2

  • adope MoNA msp format for getMSP

enviGCMS 0.7.1

  • CRAN

enviGCMS 0.7.0

  • update MDplotR shiny documents
  • change class to inherits
  • fix save issue

enviGCMS 0.6.9

  • update writeMSP function
  • add findpfc to find potential PFCs
  • add getpn to connect pos and neg mode data and return mzrt object
  • add support for xcms 3 EIC extraction
  • add getcompare to align multiple mzrt objects

enviGCMS 0.6.8

  • goodpractice check
  • spell check

enviGCMS 0.6.7

  • fix bug in getpower function
  • change default par parameters for plotmrc
  • remove the export of deprecated function
  • fix the typo in documents
  • improve getMSP to fit MoNA MSP format
  • add getalign function to align two peaks vectors and remove getoverlapmass, getoverlaprt
  • modify getmass to accept negative value
  • add getms1anno for MS1 annotation by local compounds database with predefined paired mass distances
  • add support to save target data csv without change default name
  • add retention time alignment function for peaks lists
  • add getalign2 function to align mass to charge ratio, retention time for the same peak list, this function could be used to refine peaks list
  • fix color issues in plotrla and plotridge function

enviGCMS 0.6.6

  • CRAN

enviGCMS 0.6.5

  • change to formal group information for mzrt class
  • fix log infinite issue in plotridge
  • update list data

enviGCMS 0.6.4

  • plotpeak for intensity of peaks across samples or samples across peaks
  • plotridge for ridgeline density plot
  • plotrug for 1-d density for multiple samples

enviGCMS 0.6.3

  • add findlipid to annotate lipid class based on referenced Kendrick mass defect

enviGCMS 0.6.2

  • add getMSP to read in EI-MS or MS/MS msp file as list for annotation
  • add xrankanno and dotpanno function for MS/MS X Rank and dot product annotation
  • add getrangecsv for MS2 mgf file extraction

enviGCMS 0.6.1

  • remove dependency of genefilter
  • remove dependency of reshape2
  • remove dependency of ggplot2
  • remove dependency of ggridges

enviGCMS 0.6.0

  • remove dependency of rcdk package
  • CRAN

enviGCMS 0.5.9

  • fix ... issue

enviGCMS 0.5.8

  • add functions to get and plot density weighted intensity
  • add pooled QC vignette
  • add plotcc to plot calibration curve

enviGCMS 0.5.7

  • CRAN

enviGCMS 0.5.6

  • fix group issue in mzrt object
  • all the group info will be imported as character while user could change the character into dataframe
  • export getmzrtcsv
  • add findmet to export metabolites for certain compounds based on mass defect
  • add demo data for TBBPA metabolites from this publication

enviGCMS 0.5.5

  • CRAN

enviGCMS 0.5.4

Major changes

  • move dependances of xcms and MSnbase to suggest and remove the export for those functions
  • introduce parallel computation in getdoe
  • add demo data and organize examples
  • add Relative Log Abundance (RLA) plots and Relative Log Abundance Ridge(RLA) plots
  • add getcsv to save the list as csv file
  • add getfilter to filter the list
  • add getpower to deal with power analysis in metabolomics
  • rewrite getmzrt and getdoe to make analysis easier
  • deprecated getupload, getfeaturest and getfeaturesanova
  • update vignettes
  • add support for group dim larger than 2

enviGCMS 0.5.2

Major changes

  • combine xcms and xcms 3 object function
  • add support for single group plot
  • add shiny application for mass defect analysis
  • add function to compute high order mass defect
  • add function to compare two peak list by overlap
  • add function to output csv file from list object
  • add function to perform pmd analysis
  • add function to get chemical formula
  • fix wrong object name in getmzrt/getmzrt2
  • add options to export EIC object
  • add function to screen organohalogen compounds
  • add density plot for multiple samples

enviGCMS 0.5.0

  • CRAN

Major changes from last CRAN version 0.3.4

  • use list to communicate results between function instead of xcms objects
  • getdoe function to handle data for various experimental design
  • add functions and shiny application for Short-Chain Chlorinated Paraffins analysis
  • update the visualization function
  • support xcms 3 new objects

enviGCMS 0.4.5

Major changes

  • remove GlobalStd function and shiny application into pmd package
  • remove batch correction and simulation function into mzrtsim package
  • add shiny application for sccp analysis
  • add deprecated function
  • update vignettes

enviGCMS 0.4.4

Major changes

  • Shiny application for GlobalStd
  • New GlobalStd algorithm
  • New paired analysis based on retention time hierarchical clustering, paired mass differences(PMD), PMD frequency analysis
  • Remove mass defect related analysis
  • Plot function for paired analysis
  • Plot function for GlobalStd result
  • Organize the codes

Minor changes

  • Add Mode function
  • reformat code by formatR package

enviGCMS 0.4.3

Major changes

  • RT cluster analysis for tentative isotope, adducts, and neutral loss peaks detection
  • Correlation analysis to select the feature peaks within rt groups
  • Mass defect(cluster) analysis for homologous series detection
  • Add csv file generation for simulation data
  • Add heatmap for mzrt profile
  • Add index to plotpca

Minor changes

  • Fit xcms 3 new function in getdata2
  • Change the default name for metaboanalyst
  • remove nonascll in CITATION
  • remove faahKO package and MSnbase version for cran check

enviGCMS 0.4.2

Major changes

  • update Vignette
  • add function for SCCP analysis
  • add peak list filter function based mass difference

Minor changes

  • add seealso

enviGCMS 0.4.1

Major changes

  • add batch correction methods with p-value and q-value: sva, isva
  • remove svadata and svaupload
  • add mzrtsim to simulate mzrt profile
  • add simmzrt to make simulation input data
  • add rlaplot and ridgesplot to show the distribution of the data

Minor changes

  • revise citation keywords

enviGCMS 0.4.0

Major changes

  • Add getdoe and remove former DoE related function
  • Change the plot function from xcmsset based to list based
  • Add support for xcms 3 function