Package: MetMashR 1.1.0

Gavin Rhys Lloyd

MetMashR: Metabolite Mashing with R

A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.

Authors:Gavin Rhys Lloyd [aut, cre], Ralf Johannes Maria Weber [aut]

MetMashR_1.1.0.tar.gz
MetMashR_1.1.0.zip(r-4.5)MetMashR_1.1.0.zip(r-4.4)MetMashR_1.1.0.zip(r-4.3)
MetMashR_1.1.0.tgz(r-4.4-any)MetMashR_1.1.0.tgz(r-4.3-any)
MetMashR_1.1.0.tar.gz(r-4.5-noble)MetMashR_1.1.0.tar.gz(r-4.4-noble)
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MetMashR.pdf |MetMashR.html✨
MetMashR/json (API)
NEWS

# Install 'MetMashR' in R:
install.packages('MetMashR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/computational-metabolomics/metmashr/issues

On BioConductor:MetMashR-0.99.2(bioc 3.20)

workflowstepmetabolomicskegg

5.30 score 1 stars 5 scripts 100 exports 71 dependencies

Last updated 23 days agofrom:e797206569. Checks:OK: 1 NOTE: 1 ERROR: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winERROROct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winERROROct 31 2024
R-4.4-macERROROct 31 2024
R-4.3-winERROROct 31 2024
R-4.3-macERROROct 31 2024

Exports:add_columnsadd_labelsannotation_bar_chartannotation_databaseannotation_histogramannotation_histogram2dannotation_pie_chartannotation_sourceannotation_tableannotation_upset_chartannotation_venn_chartAnnotationDb_databaseAnnotationDb_selectBiocFileCache_databasecache_as_iscalc_ppm_diffcalc_rt_diffcd_sourcechart_plotcheck_for_columnsclassyfire_lookupcombine_columnscombine_recordscombine_sourcesCompoundDb_sourcecompute_columncompute_meancompute_mediancompute_modecompute_recordcount_recordsdatabase_lookupeutils_lookupexcel_databasefilter_labelsfilter_nafilter_rangefilter_recordsfilter_vennfusefuse_uniquegithub_fileGO_databasegreek_dictionaryhmdb_lookupid_countsimport_sourceis_writablekegg_lookuplcms_tablelipidmaps_lookupls_sourcemodel_applymspurity_sourceMTox700plus_databasemwb_compound_lookupmwb_refmet_databasemwb_structuremz_matchmzrt_matchnormalise_lipidsnormalise_stringsnothingopenbabel_structureopsin_lookupPathBank_metabolite_databasepivot_columnsprioritiseprioritise_columnspubchem_compound_lookuppubchem_property_lookuppubchem_structurepubchem_widgetracemic_dictionaryrdata_databaserds_cacherds_databaseread_databaseread_sourceremove_columnsrename_columnsrequired_colsrest_apirt_matchselect_columnsselect_exactselect_gradeselect_matchselect_maxselect_minsplit_columnsplit_recordssqlite_databasetrim_whitespacetripeptide_dictionaryunique_recordsunzip_before_cachevertical_joinwhereverwrite_database

Dependencies:abindaskpassBiobaseBiocGenericsclicolorspacecowplotcrayoncurlDelayedArraydplyrevaluatefansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggthemesgluegtablehighrhttrhttr2IRangesisobandjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeontologyIndexopensslpillarpkgconfigpurrrR6rappdirsRColorBrewerrlangrolsS4ArraysS4VectorsscalesSparseArraystringistringrstructSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc

Annotation of mixtures of standards

Gavin Rhys Lloyd

Rendered fromannotate_mixtures.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-10-18
Started: 2024-01-19

Exploring the MTox700+ library

Gavin Rhys Lloyd

Rendered fromexploring_mtox.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-10-18
Started: 2024-01-19

Extending MetMashR

Gavin Rhys Lloyd

Rendered fromExtending_MetMashR.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-03-21
Started: 2024-01-19

Using MetMashR

Rendered fromusing_MetMashR.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-10-18
Started: 2024-01-19

Readme and manuals

Help Manual

Help pageTopics
Add columnsadd_columns
Add column of labelsadd_labels
Annotation bar chartannotation_bar_chart
An annotation databaseannotation_database
Annotation histogramannotation_histogram
Annotation 2D histogramannotation_histogram2d
Annotation pie chartannotation_pie_chart
An annotation sourceannotation_source
An annotation tableannotation_table
Annotation UpSet chartannotation_upset_chart
Annotation venn chartannotation_venn_chart
AnnotationDb databaseAnnotationDb_database
Select columns from AnnotationDb databaseAnnotationDb_select
Cached databaseBiocFileCache_database
Cache file with no changes using BiocFileCachecache_as_is
Calculate ppm differencecalc_ppm_diff
Calculate RT differencecalc_rt_diff
LCMS tablecd_source
chart_plot methodchart_plot chart_plot,annotation_bar_chart,annotation_source-method chart_plot,annotation_histogram,annotation_source-method chart_plot,annotation_histogram2d,annotation_source-method chart_plot,annotation_pie_chart,annotation_source-method chart_plot,annotation_upset_chart,annotation_source-method chart_plot,annotation_upset_chart,list-method chart_plot,annotation_venn_chart,annotation_source-method chart_plot,annotation_venn_chart,list-method chart_plot,mwb_structure,annotation_source-method chart_plot,openbabel_structure,annotation_source-method chart_plot,openbabel_structure,character-method chart_plot,pubchem_structure,annotation_source-method chart_plot,pubchem_widget,annotation_source-method
Check for columns in an 'annotation_source'check_for_columns check_for_columns,annotation_source-method
Query ClassyFire databaseclassyfire_lookup
Combine columnscombine_columns
Combine annotation records (rows)combine_records
Combine records helper functionscombine_records_helper_functions compute_mean compute_median compute_mode count_records fuse fuse_unique nothing prioritise select_exact select_grade select_match select_max select_min
Combine annotation sources (tables)combine_sources
Import CompDB sourceCompoundDb_source
Compute a columncompute_column
Compute a value for a recordcompute_record
ID lookup by databasedatabase_lookup
NCBI E-utils queryeutils_lookup
Excel databaseexcel_database
Filter by factor labelsfilter_labels
Filter by missing valuesfilter_na
Filter by rangefilter_range
Filter rowsfilter_records
Filter by factor levelsfilter_venn
GitHub filegithub_file
GO.dbGO_database
Greek dictionarygreek_dictionary
Compound ID lookup via pubchemhmdb_lookup
id countsid_counts
Import_sourceimport_source
Is database writableis_writable is_writable,annotation_database-method is_writable,rdata_database-method
Convert to or from kegg identifierskegg_lookup
LCMS tablelcms_table
LipidMaps api lookuplipidmaps_lookup
LCMS tablels_source
Apply methodmodel_apply model_apply,add_columns,annotation_source-method model_apply,add_labels,annotation_source-method model_apply,AnnotationDb_select,annotation_source-method model_apply,calc_ppm_diff,annotation_table-method model_apply,calc_rt_diff,annotation_table-method model_apply,combine_columns,annotation_source-method model_apply,combine_records,annotation_source-method model_apply,combine_sources,annotation_source-method model_apply,combine_sources,list-method model_apply,CompoundDb_source,annotation_source-method model_apply,compute_column,annotation_source-method model_apply,compute_record,annotation_source-method model_apply,database_lookup,annotation_source-method model_apply,filter_labels,annotation_source-method model_apply,filter_na,annotation_source-method model_apply,filter_range,annotation_source-method model_apply,filter_records,annotation_source-method model_apply,filter_venn,annotation_source-method model_apply,id_counts,annotation_source-method model_apply,import_source,annotation_source-method model_apply,kegg_lookup,annotation_source-method model_apply,model,annotation_source-method model_apply,model,list-method model_apply,model_seq,annotation_source-method model_apply,model_seq,list-method model_apply,mspurity_source,lcms_table-method model_apply,mzrt_match,lcms_table-method model_apply,mz_match,annotation_source-method model_apply,normalise_lipids,annotation_source-method model_apply,normalise_strings,annotation_source-method model_apply,pivot_columns,annotation_source-method model_apply,prioritise_columns,annotation_source-method model_apply,remove_columns,annotation_source-method model_apply,rename_columns,annotation_source-method model_apply,rest_api,annotation_source-method model_apply,rt_match,annotation_table-method model_apply,select_columns,annotation_source-method model_apply,split_column,annotation_source-method model_apply,split_records,annotation_source-method model_apply,trim_whitespace,annotation_source-method model_apply,unique_records,annotation_source-method
msPurity sourcemspurity_source
MTox700plus_databaseMTox700plus_database
Convert to/from kegg identifiersmwb_compound_lookup
mwb_refmet_databasemwb_refmet_database
MWB molecular structuremwb_structure
mz matchingmz_match
mz matchingmzrt_match
Normalise Lipids nomenclaturenormalise_lipids
Normalise stringnormalise_strings
OpenBabel molecular structureopenbabel_structure
Compound ID lookup via OPSINopsin_lookup
PathBank_metabolite_databasePathBank_metabolite_database
Pivot longerpivot_columns
Combine several columns into a single column.prioritise_columns
Compound ID lookup via PubChempubchem_compound_lookup
Compound property lookup via pubchempubchem_property_lookup
PubChem molecular structurepubchem_structure
PubChem widgetpubchem_widget
Racemic dictionaryracemic_dictionary
rdata databaserdata_database
rds cacherds_cache
rds databaserds_database
Read a databaseread_database read_database,AnnotationDb_database-method read_database,annotation_database-method read_database,BiocFileCache_database-method read_database,excel_database-method read_database,github_file-method read_database,MTox700plus_database-method read_database,mwb_refmet_database-method read_database,PathBank_metabolite_database-method read_database,rdata_database-method read_database,rds_database-method read_database,sqlite_database-method
Import annotation sourceread_source read_source,annotation_database-method read_source,annotation_source-method read_source,cd_source-method read_source,ls_source-method
Select columnsremove_columns
Select columnsrename_columns
Required columns in an annotation sourcerequired_cols required_cols,annotation_source-method
rest_apirest_api
rt matchingrt_match
Select columnsselect_columns
Split a columnsplit_column
Expand recordssplit_records
SQLite databasesqlite_database
Trim whitespacetrim_whitespace
Tripeptide dictionarytripeptide_dictionary
Keep unique_recordsunique_records
Unzip file before caching with BiocFileCache_databaseunzip_before_cache
Join sources verticallyvertical_join vertical_join,annotation_source,annotation_source-method vertical_join,list,missing-method
Filter helper function to select recordswherever
Write to a databasewrite_database write_database,annotation_database-method write_database,rds_database-method write_database,sqlite_database-method