Package: tidyproteomics 1.7.4

Jeff Jones

tidyproteomics: An S3 data object and framework for common quantitative proteomic analyses

Creates a simple, universal S3 data structure for the post analysis of mass spectrometry based quantitative proteomic data. In addition, this package collects, adapts and organizes several useful algorithms and methods used in typical post analysis workflows.

Authors:Jeff Jones [aut, cre]

tidyproteomics_1.7.4.tar.gz
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tidyproteomics_1.7.4.tgz(r-4.4-any)tidyproteomics_1.7.4.tgz(r-4.3-any)
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tidyproteomics.pdf |tidyproteomics.html
tidyproteomics/json (API)

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

Peer review:

Bug tracker:https://github.com/jeffsocal/tidyproteomics/issues

Datasets:

On CRAN:

52 exports 27 stars 2.70 score 103 dependencies

Last updated 1 months agofrom:9a0fc05105

Exports:%like%annotatecollapseenrichmentexperimentalexperimental_groupsexport_analysisexport_compexpexport_configexport_quantexpressionextractfgeomeanfmeanfmedianfminfsumget_quant_nameshdfimportimputeimpute.randomforestintersectionload_localmergenormalizeoperationspath_to_package_dataplot_compexpplot_countsplot_dynamic_rangeplot_enrichmentplot_eulerplot_heatmapplot_normalizationplot_pcaplot_proportionplot_proteinplot_quantrankplot_variation_cvplot_variation_pcaplot_vennplot_volcanoprotein_mapreassignrm.mbrsave_localsave_tableselect_normalizationshow_annotationsstr_normalizetidyproteomics

Dependencies:askpassbackportsBHBiocGenericsBiocParallelBiostringsbitbit64broomcellrangerclassclicliprcodetoolscolorspacecowplotcpp11crayoncurldata.tabledigestdoParalleldoRNGdplyre1071eulerrfansifarverfastmatchfgseaforcatsforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenSAggplot2ggrepelgluegtablehmshttrIRangesisobanditeratorsitertoolsjsonlitelabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixmgcvmimemissForestmunsellnlmeopensslpheatmappillarpkgconfigpolyclippolylabelrprettyunitsprogressproxypurrrR6randomForestRColorBrewerRcppRcppArmadilloreadrreadxlrematchrlangrngtoolsS4VectorsscalessnowstatmodstringistringrsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrwritexlXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Helper function for subsetting%like%
Align a modification to a peptide sequencealign_modification
Align a peptide sequence to a protein sequencealign_peptide
A function for evaluating expression differences between two sample sets via the limma algorithmanalysis_counts
Main function for adding annotations to a tidyproteomics data-objectannotate
Helper function to convert the data-object into a tibbleas.data.frame.tidyproteomics
helper function for normalizing a quantitative tablecenter
Check the integrity of a tidyproteomics data objectcheck_data
Helper function for iterative expression analysischeck_pairs
Check the integrity of a tidyproteomics quantitative tibblecheck_table
Build a tidyproteomics data objectcodify
Convert peptide quantitative data into protein quantitative datacollapse
Helper function to analysis between two expression testscompute_compexp
A helper function for importing peptide table datadata_import
Helper function to subset a data framedown_select
Compute protein enrichmentenrichment
A function for evaluating term enrichment via GSEAenrichment_gsea
A function for evaluating term enrichment via Wilcoxon Rank Sumenrichment_wilcoxon
Returns the data experimental set upexperimental
Main function for adding sample groupsexperimental_groups
Export the quantitative data from an tidyproteomics data-objectexport_analysis
Comparative analysis between two expression testsexport_compexp
Helper function to export the config file to current project directoryexport_config
Export the quantitative data from an tidyproteomics data-objectexport_quant
Summarize the dataexpression
Calculate expression differences between two-samplesexpression_limma
A function for evaluating expression differences between two sample sets via the limma algorithmexpression_test
Main function for extracting quantitative data from a tidyproteomics data-objectextract
Proteolytic digest a parsed fasta listfasta_digest
Get the string defined by the regexfasta_extract
The main function for parsing a fasta filefasta_parse
Proteolytic digest a sequencefasta_peptides
Get/Set the FASTA meta data regexfasta_regex
Calculates the geometric mean of a numeric vector with NAs removedfgeomean
Calculates the mean of a numeric vector with NAs removedfmean
Calculates the median of a numeric vector with NAs removedfmedian
Calculates the minimum of a numeric vector with NAs removedfmin
Calculates the sum of a numeric vector with NAs removedfsum
Helper function to get all accounting termsget_accountings
Helper function to get available termsget_annotation_terms
Helper function to get all annotations for a given termget_annotations
Get the quantitative value namesget_quant_names
Helper function to get all sample namesget_sample_names
Helper function to get available termsget_segment
Helper function to get all sample namesget_unique_variables
Helper function to get available termsget_variables
Create a crc32 hash on a vectorhash_vector
Helper function to take the head of a tibble and display as a data.framehdf
A sample tidyproteomics data objecthela_peptides
A sample tidyproteomics data objecthela_proteins
Main function for importing data to the tidyproteomics list object, see also the documentation 'vignette("importing")' and 'vignette("workflow-importing")'import
A helper function for importing peptide table dataimport_extract
A helper function for importing peptide table dataimport_mbr
A helper function for importing peptide table dataimport_remove
A helper function for importing peptide table dataimport_rename
A helper function for importing peptide table dataimport_split
A helper function for importing peptide table dataimport_validate
Main method for imputing missing valuesimpute
Helper function for calculating imputation statsimpute_ratio
Imputes missing values based on the missForest functionimpute.randomforest
Helper function extracting a subset of proteinsintersect_venn
Create a data subsetintersection
Inverse Log 2invlog2
Helper function Venn and Euler plotslist_venn
Load project specific dataload_local
match a named vector to string vectormatch_vect
Meld a tidyproteomics data object into a single tablemeld
Merge multiple tidyproteomics data-objectsmerge
Helper function merging normalized data back into the main data-objectmerge_quantitative
Main function for munging peptide data from an extracted tidyproteomics data-objectmunge_identifier
Main function for normalizing quantitative data in a tidyproteomics data-objectnormalize
Normalization function for a tidyproteomics data-objectnormalize_limma
Normalization function for a tidyproteomics data-objectnormalize_linear
Normalization function for a tidyproteomics data-objectnormalize_loess
Normalization function for a tidyproteomics data-objectnormalize_median
Normalization function for a tidyproteomics data-objectnormalize_randomforest
Normalization function for a tidyproteomics data-objectnormalize_scaled
Normalization function for a tidyproteomics data-objectnormalize_svm
Returns the data transformationsoperations
Helper function for displaying path to datapath_to_package_data
Comparative analysis between two expression testsplot_compexp
Plot the accounting of proteins. peptides, and other countsplot_counts
Plot CVs by abundanceplot_dynamic_range
Bubble plot of enrichment valuesplot_enrichment
GGplot2 extension to plot a Euler diagramplot_euler
Plot a heatmap of quantitative values by sampleplot_heatmap
Plot normalized valuesplot_normalization
Plot PCA valuesplot_pca
Plot proportional expression valuesplot_proportion
Visualize mapped sequence dataplot_protein
Plot the variation in normalized valuesplot_quantrank
Helper function for saving plotsplot_save
Plot the variation in normalized valuesplot_variation_cv
Plot the PCA variation in normalized valuesplot_variation_pca
GGplot2 extension to plot a Venn diagramplot_venn
Volcano plot of expression valuesplot_volcano
Tidy-Quant data object plot definitionplot.tidyproteomics
Tidy-Quant data object print definitionprint.tidyproteomics
Helper function for printing messagesprintln
Align a peptide data to protein sequences for visualizationprotein_map
Align a peptide data to protein sequences for visualizationprotein_map_munge
Read data by format typeread_data
A helper function for importing peptide table dataread_mzTab
reassign the sample inforeassign
Reverse the plot axis for log transformationreverselog_transformation
parallel compute function for randomforestrf_parallel
Remove MBR from the dataset across segmentsrm.mbr
Store data locallysave_local
Write table data locallysave_table
Select a normalization methodselect_normalization
set a named vectorset_vect
Display the current annotation datashow_annotations
Assess the relative amount of protein contaminationstats_contamination
Helper function for displaying datastats_print
Summarize the protein accountingstats_summary
Normalize the column names in a tibblestr_normalize
Create a data subsetsubset.tidyproteomics
Summarize the datasummary.tidyproteomics
parallel compute function for randomforestsvm_parallel
Helper function to quantitation plotstable_quantrank
helper function for having nice colorstheme_palette
Tidy-Quant data object print definitiontidyproteomics
Helper function to subset a data frametidyproteomics_quo
Helper function to get a name from the ...tidyproteomics_quo_name
Helper function to summarize the datatidyproteomics_summary
helper function for normalizing quantitative data from a tidyproteomics data-objecttransform_factor
helper function for normalizing a quantitative tabletransform_log2
helper function for normalizing quantitative data from a tidyproteomics data-objecttransform_median
Helper functio to write data table locallywrite_local