enviGCMS 0.7.1
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
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
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
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
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
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
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
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