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"available_tissue_class",
"available_tissue_type",
"check_marker",
"dge_list",
"dgeList",
"dprocess_dgeList",
"finsert",
"get_attr",
"get_marker",
"group_stat",
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"groupStat",
"groupStatI",
"limma_fit",
"limmaFit",
"list2dt",
"list2graph",
"match_ref",
"matchCellMarker2",
"plot_enrichment",
"plot_gsea",
"plot_marker_distribution",
"plot_ora",
"plot_possible_cell",
"plot_rank",
"plot_seurat_dot",
"plot_volcano",
"plotEnrichment2",
"plotGSEA",
"plotMarkerDistribution",
"plotORA",
"plotPossibleCell",
"plotRank",
"plotSeuratDot",
"plotVolcano",
"prepare_geo",
"prepare_tcga",
"process_dge_list",
"set_colnames",
"set_rownames",
"set_savedir",
"setcolnames",
"setrownames",
"setSavedir",
"split_matrix",
"suggest_best_match",
"theme_publication",
"tune_parameters",
"tuneParameters",
"uniprot_id_map",
"work_in",
"workIn"
],
"_datasets": [
{
"name": "CHOL_DEGs",
"title": "Example DEGs data from Limma-Voom workflow for TCGA-CHOL project",
"object": "CHOL_DEGs",
"class": [
"data.table",
"data.frame"
],
"fields": [
"rid",
"seqnames",
"start",
"end",
"width",
"strand",
"source",
"type",
"score",
"phase",
"gene_id",
"gene_type",
"gene_name",
"level",
"hgnc_id",
"havana_gene",
"logFC",
"AveExpr",
"t",
"P.Value",
"adj.P.Val",
"B",
"tumor_vs_normal"
],
"rows": 21938,
"table": true,
"tojson": true
},
{
"name": "pbmc.markers",
"title": "Example marker data from Seurat::FindAllMarkers()",
"object": "pbmc.markers",
"class": [
"data.frame"
],
"fields": [
"p_val",
"avg_log2FC",
"pct.1",
"pct.2",
"p_val_adj",
"cluster",
"gene"
],
"rows": 11629,
"table": true,
"tojson": true
}
],
"_help": [
{
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"title": "Visualization Artist for Custom Plots",
"topics": [
"Artist"
]
},
{
"page": "available_ele",
"title": "Extract Unique Elements from a Column with Optional Filtering",
"topics": [
"available_ele"
]
},
{
"page": "available_tissue_class",
"title": "Retrieve Available Tissue Classes for a Given Species",
"topics": [
"available_tissue_class"
]
},
{
"page": "available_tissue_type",
"title": "Retrieve Available Tissue Types for a Given Species",
"topics": [
"available_tissue_type"
]
},
{
"page": "check_marker",
"title": "Verify and Explore Cell Type Annotations",
"topics": [
"check_marker"
]
},
{
"page": "CHOL_DEGs",
"title": "Example DEGs data from Limma-Voom workflow for TCGA-CHOL project",
"topics": [
"CHOL_DEGs"
]
},
{
"page": "dge_list",
"title": "Construct a DGEList Object",
"topics": [
"dge_list"
]
},
{
"page": "dgeList",
"title": "Construct a DGEList Object (Deprecated)",
"topics": [
"dgeList"
]
},
{
"page": "dprocess_dgeList",
"title": "Filter and Normalize DGEList Data (Deprecated)",
"topics": [
"dprocess_dgeList"
]
},
{
"page": "finsert",
"title": "Create a Vector from an Index-to-Label Map",
"topics": [
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]
},
{
"page": "get_attr",
"title": "Retrieve Attributes from an R Object",
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]
},
{
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"title": "Retrieve Markers for Specific Cells from cellMarker3",
"topics": [
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]
},
{
"page": "group_stat",
"title": "Perform Summary Analysis by Group Using Regular Expressions",
"topics": [
"group_stat"
]
},
{
"page": "group_stat_i",
"title": "Perform Summary Analysis by Group Using an column Index",
"topics": [
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]
},
{
"page": "groupStat",
"title": "Summarize Data by Group Using Regular Expressions (Deprecated)",
"topics": [
"groupStat"
]
},
{
"page": "groupStatI",
"title": "Summarize Data by Group Using an Index (Deprecated)",
"topics": [
"groupStatI"
]
},
{
"page": "limma_fit",
"title": "Fit a Linear Model for RNA-seq data using limma",
"topics": [
"limma_fit"
]
},
{
"page": "limmaFit",
"title": "Fit a Linear Model for RNA-seq Data (Deprecated)",
"topics": [
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]
},
{
"page": "list2dt",
"title": "Convert a List with Vector Values to a Long Data.table",
"topics": [
"list2dt"
]
},
{
"page": "list2graph",
"title": "Convert a Named List into a Graph Based on Overlap",
"topics": [
"list2graph"
]
},
{
"page": "match_ref",
"title": "Annotate Clusters by Matching Markers with the CellMarker 3.0 Database",
"topics": [
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]
},
{
"page": "matchCellMarker2",
"title": "Annotate Clusters by Matching Markers (Deprecated)",
"topics": [
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]
},
{
"page": "pbmc.markers",
"title": "Example marker data from Seurat::FindAllMarkers()",
"topics": [
"pbmc.markers"
]
},
{
"page": "plot_enrichment",
"title": "Plot Enrichment for a Specific Pathway in fgsea",
"topics": [
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]
},
{
"page": "plot_gsea",
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"topics": [
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},
{
"page": "plot_marker_distribution",
"title": "Plot Distribution of a Marker Across Tissues and Cell Types",
"topics": [
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]
},
{
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"title": "Visualization of ORA Test Results",
"topics": [
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]
},
{
"page": "plot_possible_cell",
"title": "Plot Possible Cell Distribution Based on match_ref() Results",
"topics": [
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]
},
{
"page": "plot_rank",
"title": "Visualization of GSEA Rank Statistics",
"topics": [
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]
},
{
"page": "plot_seurat_dot",
"title": "Create a Dot Plot to Visualize Marker Gene Expression",
"topics": [
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},
{
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},
{
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},
{
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"title": "Visualize GSEA Results (Deprecated)",
"topics": [
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},
{
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"topics": [
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},
{
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},
{
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]
},
{
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"topics": [
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]
},
{
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"title": "Create a Dot Plot of Marker Gene Expression (Deprecated)",
"topics": [
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{
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"topics": [
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]
},
{
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{
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{
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{
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"title": "Rename Column Names of a Data Frame or Matrix",
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"title": "Rename Row Names of a Data Frame or Matrix",
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"title": "Set a Directory for Saving Files",
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{
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"title": "Split a Matrix into Smaller Sub-matrices by Column or Row",
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},
{
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"topics": [
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},
{
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"title": "Custom ggplot2 Theme for Academic Publications",
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},
{
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"title": "Optimize Resolution and Gene Number Parameters for Cell Type Annotation",
"topics": [
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},
{
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{
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],
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