Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

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Documentation for package ‘easybio’ version 1.3.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

Artist	Visualization Artist for Custom Plots
available_ele	Extract Unique Elements from a Column with Optional Filtering
available_tissue_class	Retrieve Available Tissue Classes for a Given Species
available_tissue_type	Retrieve Available Tissue Types for a Given Species
check_marker	Verify and Explore Cell Type Annotations
CHOL_DEGs	Example DEGs data from Limma-Voom workflow for TCGA-CHOL project
dgeList	Construct a DGEList Object (Deprecated)
dge_list	Construct a DGEList Object
dprocess_dgeList	Filter and Normalize DGEList Data (Deprecated)
finsert	Create a Vector from an Index-to-Label Map
get_attr	Retrieve Attributes from an R Object
get_marker	Retrieve Markers for Specific Cells from cellMarker3
groupStat	Summarize Data by Group Using Regular Expressions (Deprecated)
groupStatI	Summarize Data by Group Using an Index (Deprecated)
group_stat	Perform Summary Analysis by Group Using Regular Expressions
group_stat_i	Perform Summary Analysis by Group Using an column Index
limmaFit	Fit a Linear Model for RNA-seq Data (Deprecated)
limma_fit	Fit a Linear Model for RNA-seq data using limma
list2dt	Convert a List with Vector Values to a Long Data.table
list2graph	Convert a Named List into a Graph Based on Overlap
matchCellMarker2	Annotate Clusters by Matching Markers (Deprecated)
match_ref	Annotate Clusters by Matching Markers with the CellMarker 3.0 Database
pbmc.markers	Example marker data from Seurat::FindAllMarkers()
plotEnrichment2	Plot Enrichment for a Pathway (Deprecated)
plotGSEA	Visualize GSEA Results (Deprecated)
plotMarkerDistribution	Plot Distribution of a Marker (Deprecated)
plotORA	Visualize ORA Test Results (Deprecated)
plotPossibleCell	Plot Possible Cell Distribution (Deprecated)
plotRank	Visualize GSEA Rank Statistics (Deprecated)
plotSeuratDot	Create a Dot Plot of Marker Gene Expression (Deprecated)
plotVolcano	Plot a Volcano Plot (Deprecated)
plot_enrichment	Plot Enrichment for a Specific Pathway in fgsea
plot_gsea	Visualization of GSEA Result from 'fgsea::fgsea()'
plot_marker_distribution	Plot Distribution of a Marker Across Tissues and Cell Types
plot_ora	Visualization of ORA Test Results
plot_possible_cell	Plot Possible Cell Distribution Based on match_ref() Results
plot_rank	Visualization of GSEA Rank Statistics
plot_seurat_dot	Create a Dot Plot to Visualize Marker Gene Expression
plot_volcano	Plot Volcano Plot for Differentially Expressed Genes
prepare_geo	Download and Process GEO Data
prepare_tcga	Prepare TCGA Data for Analysis
process_dge_list	Filter Low-Expressed Genes and Normalize DGEList Data
setcolnames	Rename Column Names (Deprecated)
setrownames	Rename Row Names (Deprecated)
setSavedir	Set a Directory for Saving Files (Deprecated)
set_colnames	Rename Column Names of a Data Frame or Matrix
set_rownames	Rename Row Names of a Data Frame or Matrix
set_savedir	Set a Directory for Saving Files
split_matrix	Split a Matrix into Smaller Sub-matrices by Column or Row
suggest_best_match	Suggest Best Matches for a String from a Vector of Choices
theme_publication	Custom ggplot2 Theme for Academic Publications
tuneParameters	Tune Parameters for Cell Type Annotation (Deprecated)
tune_parameters	Optimize Resolution and Gene Number Parameters for Cell Type Annotation
uniprot_id_map	Map UniProt IDs to Other Identifiers
workIn	Perform Operations in a Directory (Deprecated)
work_in	Perform Operations in a Specified Directory and Return to the Original Directory