Archive package for papers

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

CRAN version

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

CRAN version

• 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

CRAN version

enviGCMS 0.5.5

• 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
• 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

CRAN version

• add functions and shiny application for Short-Chain Chlorinated Paraffins analysis

Generalise the xcmsset based function

• Add getdoe and remove former DoE related function
• Change the plot function from xcmsset based to list based
• Add support for xcms 3 function
• Former related functions could be found in xsetplus package here: https://github.com/yufree/xsetplus