Package: mastR 1.5.0
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:
mastR_1.5.0.tar.gz
mastR_1.5.0.zip(r-4.5)mastR_1.5.0.zip(r-4.4)mastR_1.5.0.zip(r-4.3)
mastR_1.5.0.tgz(r-4.4-any)mastR_1.5.0.tgz(r-4.3-any)
mastR_1.5.0.tar.gz(r-4.5-noble)mastR_1.5.0.tar.gz(r-4.4-noble)
mastR_1.5.0.tgz(r-4.4-emscripten)mastR_1.3.5.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/davislaboratory/mastr/issues
- 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-1.5.0(bioc 3.20)mastR-1.4.0(bioc 3.19)
Last updated 2 months agofrom:f99d37b301
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:abindannotateAnnotationDbiAnnotationHubaskpassbackportsBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbootbroomcachemcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crayoncurlDBIdbplyrDelayedArraydigestdotCall64dplyredgeRExperimentHubfansifarverfastmapfilelockfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifglobalsgluegraphgridExtraGSEABasegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmalistenvlme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamsigdbmunsellnlmenloptrnnetnumDerivopensslorg.Hs.eg.dborg.Mm.eg.dbparallellypatchworkpbkrtestpillarpkgconfigplogrpngpolynomprogressrpurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrlangRSQLiterstatixS4ArraysS4VectorsscalesSeuratObjectSingleCellExperimentspspamSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 pipeline | de_analysis |
| return DEGs UP and DOWN list based on intersection or union of comparisons | DEGs_Group |
| return DEGs UP and DOWN list based on Rank Product | DEGs_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 statistics | get_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 groups | get_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 LM22 | get_lm_sig |
| Extract immune subset markers from PanglaoDB website. | get_panglao_sig |
| Convert gene-set list into GeneSetCollection | gls2gsc gls2gsc,list-method gls2gsc,vector-method |
| Make upset plot for given gene sets | gsc_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 PCs | pca_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 PCs | pca_matrix_plot_init |
| plot diagnostics before and after 'process_data()' | plot_diagnostics |
| plot Mean-variance trend after voom and after final linear fit | plot_mean_var |
| Single PCA plot function | plotPCAbiplot |
| process data | process_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 factors | pseudo_sample_list |
| Aggregate single cells to pseudo-samples according to specific factors | pseudo_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 comparisons | select_sig |
| Boxplot of median expression or scores of signature | sig_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 signature | sig_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 density | sig_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 others | sig_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::treat | voom_fit_treat |
