Package: MOSuite 0.3.1.9000

MOSuite: R package for differential multi-omics analysis

Multi-Omics Suite provides a suite of functions to clean, filter, batch-correct, normalize, visualize, and perform differential analysis. While the package is designed for differential RNA-seq analysis and multi-omics datasets, it can be used for any data represented in a counts table. See the website for more information, documentation, and examples at <https://ccbr.github.io/MOSuite/>.

Authors:Kelly Sovacool [aut, cre], Philip Homan [aut], Vishal Koparde [aut], Samantha Chill [aut], T. Joshua Meyer [ctb], CCR Collaborative Bioinformatics Resource [cph]

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manual.pdf |manual.html✨
card.svg |card.png
MOSuite/json (API)
NEWS

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

Bug tracker:https://github.com/ccbr/mosuite/issues

Pkgdown/docs site:https://ccbr.github.io

Datasets:
  • gene_counts - RSEM expected gene counts
  • nidap_batch_corrected_counts - Batch-corrected counts for the NIDAP test dataset.
  • nidap_batch_corrected_counts_2 - Batch-corrected counts for the NIDAP test dataset. The result of running 'batch_correct_counts()' on 'nidap_norm_counts'.
  • nidap_clean_raw_counts - Clean raw counts for the NIDAP test dataset. The result of running 'clean_raw_counts()' on 'nidap_raw_counts'.
  • nidap_deg_analysis - Differential gene expression analysis for the NIDAP test dataset.
  • nidap_deg_analysis_2 - Differential gene expression analysis for the NIDAP test dataset. The result of running 'diff_counts()' on 'nidap_filtered_counts'.
  • nidap_deg_gene_list - List of differentially expressed genes from the NIDAP test dataset using default parameters with 'filter_diff()'.
  • nidap_filtered_counts - Filtered counts for the NIDAP test dataset. The result of running 'filter_counts()' on 'nidap_clean_raw_counts'.
  • nidap_norm_counts - Normalized counts for the NIDAP test dataset. The result of running 'normalize_counts()' on 'nidap_filtered_counts'.
  • nidap_raw_counts - Raw counts for the NIDAP test dataset Pairs with 'nidap_sample_metadata'.
  • nidap_sample_metadata - Sample metadata for the NIDAP test dataset
  • nidap_venn_diagram_dat - Output data from venn diagram. The result of running 'plot_venn_diagram()' on 'nidap_volcano_summary_dat'
  • nidap_volcano_summary_dat - Summarized differential expression analysis for input to venn diagram

On CRAN:

Conda:

4.31 score 2 stars 15 scripts 42 exports 101 dependencies

Last updated from:241d50fc48. Checks:8 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR200
source / vignettesERROR343
linux-release-x86_64ERROR210
macos-release-arm64ERROR91
macos-oldrel-arm64ERROR124
windows-develERROR166
windows-releaseERROR125
windows-oldrelERROR121
wasm-releaseOK184

Exports::=!!.databatch_correct_countsbind_dfs_longcalc_cpmcalc_pcaclean_raw_countscli_execcli_from_jsoncreate_multiOmicDataSet_from_dataframescreate_multiOmicDataSet_from_filesdiff_countsdo_mathextract_countsfilter_countsfilter_diffget_colors_lstget_colors_vctrjoin_dfs_wideload_moo_from_data_dirmultiOmicDataSetnormalize_countsparse_optional_vectorparse_samples_to_renameparse_vector_with_defaultplot_corr_heatmapplot_expr_heatmapplot_histogramplot_pcaplot_pca_2dplot_pca_3dplot_read_depthplot_venn_diagramplot_volcano_enhancedplot_volcano_summaryprint_or_save_plotread_multiOmicDataSetset_color_palsetup_capsule_environmentwrite_multiOmicDataSetwrite_multiOmicDataSet_properties

Dependencies:abindaskpassassertthatbase64encBHBiobaseBiocGenericsBiocParallelbslibcachemclicodetoolscpp11crosstalkcurldata.tableDelayedArraydendextendDESeq2digestdplyredgeRevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopenssloptionsotelpillarpkgconfigplotlyplyrpromisespurrrR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Perform batch correctionbatch_correct_counts
Bind dataframes in named list to long dataframebind_dfs_long
Calculate counts-per-million (CPM) on raw counts in a multiOmicDataSetcalc_cpm
Perform principal components analysiscalc_pca
Clean Raw Countsclean_raw_counts
Construct a multiOmicDataSet object from data framescreate_multiOmicDataSet_from_dataframes
Construct a multiOmicDataSet object from text files (e.g. TSV, CSV).create_multiOmicDataSet_from_files
Differential expression analysisdiff_counts
Extract count dataextract_counts extract_counts,MOSuite::multiOmicDataSet-method
Filter low countsfilter_counts
Filter features from differential analysis based on statistical significancefilter_diff
RSEM expected gene countsgene_counts
Create named list of default colors for plottingget_colors_lst
Get vector of colors for observations in one column of a data frameget_colors_vctr
Join dataframes in named list to wide dataframejoin_dfs_wide
multiOmicDataSet classmultiOmicDataSet
Batch-corrected counts for the NIDAP test dataset.nidap_batch_corrected_counts
Batch-corrected counts for the NIDAP test dataset. The result of running 'batch_correct_counts()' on 'nidap_norm_counts'.nidap_batch_corrected_counts_2
Clean raw counts for the NIDAP test dataset. The result of running 'clean_raw_counts()' on 'nidap_raw_counts'.nidap_clean_raw_counts
Differential gene expression analysis for the NIDAP test dataset.nidap_deg_analysis
Differential gene expression analysis for the NIDAP test dataset. The result of running 'diff_counts()' on 'nidap_filtered_counts'.nidap_deg_analysis_2
List of differentially expressed genes from the NIDAP test dataset using default parameters with 'filter_diff()'.nidap_deg_gene_list
Filtered counts for the NIDAP test dataset. The result of running 'filter_counts()' on 'nidap_clean_raw_counts'.nidap_filtered_counts
Normalized counts for the NIDAP test dataset. The result of running 'normalize_counts()' on 'nidap_filtered_counts'.nidap_norm_counts
Raw counts for the NIDAP test dataset Pairs with 'nidap_sample_metadata'.nidap_raw_counts
Sample metadata for the NIDAP test datasetnidap_sample_metadata
Output data from venn diagram. The result of running 'plot_venn_diagram()' on 'nidap_volcano_summary_dat'nidap_venn_diagram_dat
Summarized differential expression analysis for input to venn diagramnidap_volcano_summary_dat
Normalize countsnormalize_counts
MOSuite Optionsoptions
Plot correlation heatmapplot_corr_heatmap
Plot correlation heatmap for counts dataframeplot_corr_heatmap,data.frame-method plot_corr_heatmap.data.frame
Plot correlation heatmap for multiOmicDataSetplot_corr_heatmap,MOSuite::multiOmicDataSet-method plot_corr_heatmap.multiOmicDataSet
Plot expression heatmapplot_expr_heatmap plot_expr_heatmap,data.frame-method plot_expr_heatmap,MOSuite::multiOmicDataSet-method
Plot histogramplot_histogram
Plot histogram for counts dataframeplot_histogram,data.frame-method plot_histogram.data.frame
Plot histogram for multiOmicDataSetplot_histogram,MOSuite::multiOmicDataSet-method plot_histogram.multiOmicDataSet
Perform and plot a Principal Components Analysisplot_pca
Perform and plot a 2D Principal Components Analysisplot_pca_2d plot_pca_2d,data.frame-method plot_pca_2d,MOSuite::multiOmicDataSet-method
Perform and plot a 3D Principal Components Analysisplot_pca_3d plot_pca_3d,data.frame-method plot_pca_3d,MOSuite::multiOmicDataSet-method
Plot 2D or 3D PCA for counts dataframeplot_pca,data.frame-method plot_pca.data.frame
Plot 2D or 3D PCA for multiOmicDatasetplot_pca,MOSuite::multiOmicDataSet-method plot_pca.multiOmicDataSet
Plot read depth as a bar plotplot_read_depth
Plot read depth for 'data.frame'plot_read_depth,data.frame-method plot_read_depth.data.frame
Plot read depth for multiOmicDataSetplot_read_depth,MOSuite::multiOmicDataSet-method plot_read_depth.multiOmicDataSet
Plot a venn diagram, UpSet plot, or table of intersectionsplot_venn_diagram plot_venn_diagram,data.frame-method plot_venn_diagram,MOSuite::multiOmicDataSet-method
Enhanced Volcano Plotplot_volcano_enhanced plot_volcano_enhanced,data.frame-method plot_volcano_enhanced,MOSuite::multiOmicDataSet-method
Volcano Plot - Summaryplot_volcano_summary plot_volcano_summary,data.frame-method plot_volcano_summary,MOSuite::multiOmicDataSet-method
Print and/or save a ggplotprint_or_save_plot
Read a multiOmicDataSet from diskread_multiOmicDataSet
Set color palette for a single group/columnset_color_pal
Write a multiOmicDataSet to disk as an RDS filewrite_multiOmicDataSet
Write multiOmicDataSet properties to disk as CSV fileswrite_multiOmicDataSet_properties write_multiOmicDataSet_properties,MOSuite::multiOmicDataSet-method