Package: mastR 1.7.0

Jinjin Chen

mastR: Markers Automated Screening Tool in R

mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology.

Authors:Jinjin Chen [aut, cre], Ahmed Mohamed [aut, ctb], Chin Wee Tan [ctb]

mastR_1.7.0.tar.gz
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mastR.pdf |mastR.html✨
mastR/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/davislaboratory/mastr/issues

Pkgdown:https://davislaboratory.github.io

Datasets:
  • ccle_crc_5 - RNA-seq TPM data of 5 CRC cell line samples from CCLE.
  • im_data_6 - RNA-seq TMM normalized counts data of 6 sorted immune subsets.
  • lm22 - LM22 matrix for CIBERSORT.
  • lm7 - LM7 matrix for CIBERSORT.
  • msigdb_gobp_nk - Sub-collection of MSigDB gene sets.
  • nk_markers - NK cell markers combination.

On BioConductor:mastR-1.7.0(bioc 3.21)mastR-1.6.0(bioc 3.20)

softwaregeneexpressiontranscriptomicsdifferentialexpressionvisualization

4.20 score 4 stars 3 scripts 370 downloads 27 exports 140 dependencies

Last updated 2 months agofrom:492c7959f7. Checks:ERROR: 7. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 29 2024
R-4.5-winERRORNov 29 2024
R-4.5-linuxERRORNov 29 2024
R-4.4-winERRORNov 29 2024
R-4.4-macERRORNov 29 2024
R-4.3-winERRORNov 29 2024
R-4.3-macERRORNov 29 2024

Exports:ccle_2_widede_analysisfilter_subset_sigget_de_tableget_degsget_gsc_sigget_lm_sigget_panglao_siggls2gscgsc_plotlist_panglao_organslist_panglao_typesmerge_markerspca_matrix_plotplot_diagnosticsplot_mean_varprocess_datapseudo_sample_listpseudo_samplesremove_bg_expremove_bg_exp_matselect_sigsig_boxplotsig_gseaplotsig_heatmapsig_rankdensity_plotsig_scatter_plot

Dependencies:abindannotateAnnotationDbiAnnotationHubaskpassbackportsBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbootbroomcachemcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crayoncurlDBIdbplyrDelayedArrayDerivdigestdoBydotCall64dplyredgeRExperimentHubfansifarverfastmapfilelockFormulafuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifglobalsgluegraphgridExtraGSEABasegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmalistenvlme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmsigdbmunsellnlmenloptrnnetnumDerivopensslorg.Hs.eg.dborg.Mm.eg.dbparallellypatchworkpbkrtestpillarpkgconfigplogrpngpolynomprogressrpurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrlangRSQLiterstatixS4ArraysS4VectorsscalesSeuratObjectSingleCellExperimentspspamSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectoryamlzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Convert CCLE data from long data to wide data.ccle_2_wide
RNA-seq TPM data of 5 CRC cell line samples from CCLE.ccle_crc_5
DE analysis pipelinede_analysis
return DEGs UP and DOWN list based on intersection or union of comparisonsDEGs_Group
return DEGs UP and DOWN list based on Rank ProductDEGs_RP
Filter specific cell type signature genes against other subsets.filter_subset_sig filter_subset_sig,ANY-method filter_subset_sig,DGEList-method filter_subset_sig,list-method
Get DE analysis result table(s) with statisticsget_de_table get_de_table,DGEList,character,character-method get_de_table,ExpressionSet,character,character-method get_de_table,Matrix,vector,character-method get_de_table,matrix,vector,character-method get_de_table,Seurat,character,character-method get_de_table,SummarizedExperiment,character,character-method
Get differentially expressed genes by comparing specified groupsget_degs get_degs,DGEList,character,character-method get_degs,ExpressionSet,character,character-method get_degs,Matrix,vector,character-method get_degs,matrix,vector,character-method get_degs,Seurat,character,character-method get_degs,SummarizedExperiment,character,character-method
Collect genes from MSigDB or provided GeneSetCollection.get_gsc_sig get_gsc_sig,character,character-method get_gsc_sig,GeneSetCollection,character-method
Extract specific subset markers from LM7 or/and LM22get_lm_sig
Extract immune subset markers from PanglaoDB website.get_panglao_sig
Convert gene-set list into GeneSetCollectiongls2gsc gls2gsc,list-method gls2gsc,vector-method
Make upset plot for given gene setsgsc_plot
RNA-seq TMM normalized counts data of 6 sorted immune subsets.im_data_6
Show the summary info of available organs in PanglaoDB.list_panglao_organs
Show the summary info of available cell types in PanglaoDB.list_panglao_types
LM22 matrix for CIBERSORT.lm22
LM7 matrix for CIBERSORT.lm7
Merge markers list into one.merge_markers
Sub-collection of MSigDB gene sets.msigdb_gobp_nk
NK cell markers combination.nk_markers
Make a matrix plot of PCA with top PCspca_matrix_plot pca_matrix_plot,data.frame-method pca_matrix_plot,DGEList-method pca_matrix_plot,ExpressionSet-method pca_matrix_plot,Matrix-method pca_matrix_plot,matrix-method pca_matrix_plot,Seurat-method pca_matrix_plot,SummarizedExperiment-method
Make a matrix plot of PCA with top PCspca_matrix_plot_init
plot diagnostics before and after 'process_data()'plot_diagnostics
plot Mean-variance trend after voom and after final linear fitplot_mean_var
Single PCA plot functionplotPCAbiplot
process dataprocess_data process_data,DGEList,character,character-method process_data,ExpressionSet,character,character-method process_data,Matrix,vector,character-method process_data,matrix,vector,character-method process_data,Seurat,character,character-method process_data,SummarizedExperiment,character,character-method
Split cells according to specific factorspseudo_sample_list
Aggregate single cells to pseudo-samples according to specific factorspseudo_samples pseudo_samples,matrix,data.frame-method pseudo_samples,matrix,vector-method pseudo_samples,Seurat,character-method pseudo_samples,SummarizedExperiment,character-method
Remove markers with high signal in background data.remove_bg_exp remove_bg_exp,ANY,ANY,vector-method remove_bg_exp,ANY,character,vector-method remove_bg_exp,ANY,DGEList,vector-method remove_bg_exp,ANY,ExpressionSet,vector-method remove_bg_exp,ANY,missing,vector-method remove_bg_exp,ANY,Seurat,vector-method remove_bg_exp,ANY,SummarizedExperiment,vector-method remove_bg_exp,DGEList,matrix,vector-method remove_bg_exp,matrix,matrix,vector-method
Remove genes show high signal in the background expression data from markers.remove_bg_exp_mat
select DEGs from multiple comparisonsselect_sig
Boxplot of median expression or scores of signaturesig_boxplot sig_boxplot,data.frame,vector,vector,character-method sig_boxplot,DGEList,vector,character,character-method sig_boxplot,ExpressionSet,vector,character,character-method sig_boxplot,list,vector,character,character-method sig_boxplot,Matrix,vector,vector,character-method sig_boxplot,matrix,vector,vector,character-method sig_boxplot,Seurat,vector,character,character-method sig_boxplot,SummarizedExperiment,vector,character,character-method
Visualize GSEA result with input list of gene symbols.sig_gseaplot sig_gseaplot,ANY,ANY-method sig_gseaplot,DGEList,ANY-method sig_gseaplot,list,ANY-method sig_gseaplot,MArrayLM,list-method sig_gseaplot,MArrayLM,vector-method
Heatmap original markers and screened signaturesig_heatmap sig_heatmap,data.frame,ANY,vector,ANY-method sig_heatmap,DGEList,ANY,character,ANY-method sig_heatmap,ExpressionSet,ANY,character,ANY-method sig_heatmap,list,ANY,character,ANY-method sig_heatmap,Matrix,ANY,vector,ANY-method sig_heatmap,matrix,character,vector,missing-method sig_heatmap,matrix,character,vector,vector-method sig_heatmap,matrix,list,vector,missing-method sig_heatmap,Seurat,ANY,character,ANY-method sig_heatmap,SummarizedExperiment,ANY,character,ANY-method
Plot rank densitysig_rankdensity_plot sig_rankdensity_plot,data.frame,vector,vector-method sig_rankdensity_plot,DGEList,vector,character-method sig_rankdensity_plot,ExpressionSet,vector,character-method sig_rankdensity_plot,list,vector,character-method sig_rankdensity_plot,Matrix,vector,vector-method sig_rankdensity_plot,matrix,vector,vector-method sig_rankdensity_plot,Seurat,vector,character-method sig_rankdensity_plot,SummarizedExperiment,vector,character-method
Scatter plot of signature for specific subset vs otherssig_scatter_plot sig_scatter_plot,DGEList,vector,character,character-method sig_scatter_plot,ExpressionSet,vector,character,character-method sig_scatter_plot,list,vector,character,character-method sig_scatter_plot,Matrix,vector,vector,character-method sig_scatter_plot,matrix,vector,vector,character-method sig_scatter_plot,Seurat,vector,character,character-method sig_scatter_plot,SummarizedExperiment,vector,character,character-method
return DGEList containing vfit by limma::voom (if normalize = TRUE) and tfit by limma::treatvoom_fit_treat