Package: TOmicsVis 2.1.1

TOmicsVis: TOmicsVis An All-in-One Transcriptomic Analysis and Visualization R Package with shinyapp Interface

Transcriptome visualization from sample trait statistics to gene expression analysis. Six categories include "Samples Statistics", "Traits Analysis", "Differential Expression Analysis", "Advanced Analysis", "GO and KEGG Enrichment", "Tables Operations", with complete sample data.

Authors:Benben Miao [aut, cre], Wei Dong [aut]

TOmicsVis_2.1.1.tar.gz
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TOmicsVis.pdf |TOmicsVis.html✨
TOmicsVis/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/benben-miao/tomicsvis/issues

Datasets:
  • degs_lists - Paired comparisons differentially expressed genes (degs) among groups.
  • degs_stats - All DEGs of paired comparison CT-vs-LT12 stats dataframe.
  • degs_stats2 - All DEGs of paired comparison CT-vs-LT12 stats2 dataframe.
  • gene_expression - All genes in all samples expression dataframe of RNA-Seq.
  • gene_expression2 - Shared DEGs of all paired comparisons in all samples expression dataframe of RNA-Seq.
  • gene_expression3 - Shared DEGs of all paired comparisons in all groups expression dataframe of RNA-Seq.
  • gene_go_kegg - GO and KEGG annotation of background genes.
  • gene_go_kegg2 - GO and KEGG annotation of background genes.
  • network_data - Network data from WGCNA tan module top-200 dataframe.
  • samples_groups - Samples and groups for gene expression.
  • survival_data - Survival data as example data for survival_plot function.
  • traits_sex - Length, Width, Weight, and Sex traits dataframe.
  • weight_sex - Weight and Sex traits dataframe.

On CRAN:

bioinformaticspipelinerna-seqtranscriptomicsvisualization

5.81 score 57 stars 113 scripts 250 downloads 40 exports 245 dependencies

Last updated 11 months agofrom:60bb8a6e2a. Checks:ERROR: 5 WARNING: 2. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 10 2024
R-4.5-winERRORNov 10 2024
R-4.5-linuxERRORNov 10 2024
R-4.4-winERRORNov 10 2024
R-4.4-macERRORNov 10 2024
R-4.3-winWARNINGNov 10 2024
R-4.3-macWARNINGNov 10 2024

Exports:box_plotchord_plotcircos_heatmapcorr_heatmapdendro_plotflower_plotgene_cluster_trendgene_rank_plotgo_enrichgo_enrich_bargo_enrich_dotgo_enrich_netgo_enrich_statheatmap_clusterheatmap_groupkegg_enrichkegg_enrich_barkegg_enrich_dotkegg_enrich_netma_plotnetwork_plotpca_analysispca_plotquantile_plotsurvival_plottable_crosstable_filtertable_mergetable_splittomicsvistrend_plottsne_analysistsne_plotumap_analysisumap_plotupsetr_plotvenn_plotviolin_plotvolcano_plotwgcna_pipeline

Dependencies:abindadmiscAnnotationDbiapeaplotaskpassbackportsbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbootbroombslibcachemcarcarDatacheckmatecirclizeclasscliclueclusterclusterProfilercodetoolscolorspacecommonmarkComplexHeatmapcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdendextendDerivdigestdoBydoParallelDOSEdplyrDTdynamicTreeCutDynDoce1071ellipseemmeansEnhancedVolcanoenrichplotestimabilityevaluateexactRankTestsfactoextraFactoMineRfansifarverfastclusterfastmapfastmatchfgseaflashClustfontawesomeforcatsforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGetoptLongGGallyggcorrplotggforceggfunggnewscaleggplot2ggplotifyggpolypathggpubrggrepelggsciggsignifggstatsggtangleggtextggtreeGlobalOptionsglueGO.dbGOSemSimgridExtragridGraphicsgridtextgsongtableherehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrigraphimputeIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTkm.ciKMsurvknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelme4magrittrmarkdownMASSMatrixMatrixModelsmatrixStatsmaxstatmemoiseMfuzzmgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpermutepheatmappillarpkgconfigplogrplotrixplyrpngpolyclippolynompreprocessCoreprettyunitsprogresspromisesproxypurrrquantregqvalueR.methodsS3R.ooR.utilsR6randomcoloRrappdirsRColorBrewerRcppRcppEigenRcppTOMLreshape2reticulaterjsonrlangrmarkdownrpartrprojrootRSpectraRSQLiterstatixrstudioapiRtsneS4Vectorssassscalesscatterpiescatterplot3dshapeshinysnowsourcetoolsSparseMstringistringrsurvivalsurvminersurvMiscsyssystemfontstibbletidyrtidyselecttidytreetinytextkWidgetstreeiotweenrUCSC.utilsumapUpSetRutf8V8vctrsveganvennviridisviridisLiteWGCNAwidgetToolswithrxfunxml2xtableXVectoryamlyulab.utilszlibbioczoo

Readme and manuals

Help Manual

Help pageTopics
Box plot support two levels and multiple groups with P value.box_plot
Chord plot for visualizing the relationships of pathways and genes.chord_plot
Circos heatmap plot for visualizing gene expressing in multiple samples.circos_heatmap
Correlation Heatmap for samples/groups based on Pearson algorithm.corr_heatmap
Paired comparisons differentially expressed genes (degs) among groups.degs_lists
All DEGs of paired comparison CT-vs-LT12 stats dataframe.degs_stats
All DEGs of paired comparison CT-vs-LT12 stats2 dataframe.degs_stats2
Dendrograms for multiple samples/groups clustering.dendro_plot
Flower plot for stat common and unique gene among multiple sets.flower_plot
Gene cluster trend plot for visualizing gene expression trend profile in multiple samples.gene_cluster_trend
All genes in all samples expression dataframe of RNA-Seq.gene_expression
Shared DEGs of all paired comparisons in all samples expression dataframe of RNA-Seq.gene_expression2
Shared DEGs of all paired comparisons in all groups expression dataframe of RNA-Seq.gene_expression3
GO and KEGG annotation of background genes.gene_go_kegg
GO and KEGG annotation of background genes.gene_go_kegg2
Gene ranking dotplot for visualizing differentailly expressed genes.gene_rank_plot
GO enrichment analysis based on GO annotation results (None/Exist Reference Genome).go_enrich
GO enrichment analysis and bar plot (None/Exist Reference Genome).go_enrich_bar
GO enrichment analysis and dot plot (None/Exist Reference Genome).go_enrich_dot
GO enrichment analysis and net plot (None/Exist Reference Genome).go_enrich_net
GO enrichment analysis and stat plot (None/Exist Reference Genome).go_enrich_stat
Heatmap cluster for visualizing clustered gene expression data.heatmap_cluster
Heatmap group for visualizing grouped gene expression data.heatmap_group
KEGG enrichment analysis based on KEGG annotation results (None/Exist Reference Genome).kegg_enrich
KEGG enrichment analysis and bar plot (None/Exist Reference Genome).kegg_enrich_bar
KEGG enrichment analysis and dot plot (None/Exist Reference Genome).kegg_enrich_dot
KEGG enrichment analysis and net plot (None/Exist Reference Genome).kegg_enrich_net
MversusA plot for visualizing differentially expressed genes.ma_plot
Network data from WGCNA tan module top-200 dataframe.network_data
Network plot for analyzing and visualizing relationship of genes.network_plot
PCA dimensional reduction analysis for RNA-Seq.pca_analysis
PCA dimensional reduction visualization for RNA-Seq.pca_plot
Quantile plot for visualizing data distribution.quantile_plot
Samples and groups for gene expression.samples_groups
Survival data as example data for survival_plot function.survival_data
Survival plot for analyzing and visualizing survival data.survival_plot
Table cross used to cross search and merge results in two tables.table_cross
Table filter used to filter row by column condition.table_filter
Table merge used to merge multiple variables to on variable.table_merge
Table split used for splitting a grouped column to multiple columns.table_split
TOmicsVis shiny app start function.tomicsvis
Length, Width, Weight, and Sex traits dataframe.traits_sex
Trend plot for visualizing gene expression trend profile in multiple traits.trend_plot
TSNE analysis for analyzing and visualizing TSNE algorithm.tsne_analysis
TSNE plot for analyzing and visualizing TSNE algorithm.tsne_plot
UMAP analysis for analyzing RNA-Seq data.umap_analysis
UMAP plot for analyzing and visualizing UMAP algorithm.umap_plot
UpSet plot for stat common and unique gene among multiple sets.upsetr_plot
Venn plot for stat common and unique gene among multiple sets.venn_plot
Violin plot support two levels and multiple groups with P value.violin_plot
Volcano plot for visualizing differentailly expressed genes.volcano_plot
Weight and Sex traits dataframe.weight_sex
WGCNA analysis pipeline for RNA-Seq.wgcna_pipeline