Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

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Documentation for package ‘easybio’ version 1.2.1

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

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
dprocess_dgeList	Filter Low-Expressed Genes and Normalize DGEList Data
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 cellMarker2
groupStat	Perform Summary Analysis by Group Using Regular Expressions
groupStatI	Perform Summary Analysis by Group Using an column Index
limmaFit	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 with the CellMarker2.0 Database
pbmc.markers	Example marker data from Seurat::FindAllMarkers()
plotEnrichment2	Plot Enrichment for a Specific Pathway in fgsea
plotGSEA	Visualization of GSEA Result from 'fgsea::fgsea()'
plotMarkerDistribution	Plot Distribution of a Marker Across Tissues and Cell Types
plotORA	Visualization of ORA Test Results
plotPossibleCell	Plot Possible Cell Distribution Based on matchCellMarker2() Results
plotRank	Visualization of GSEA Rank Statistics
plotSeuratDot	Create a Dot Plot to Visualize Marker Gene Expression
plotVolcano	Plot Volcano Plot for Differentially Expressed Genes
prepare_geo	Download and Process GEO Data
prepare_tcga	Prepare TCGA Data for Analysis
setcolnames	Rename Column Names of a Data Frame or Matrix
setrownames	Rename Row Names of a Data Frame or Matrix
setSavedir	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	Optimize Resolution and Gene Number Parameters for Cell Type Annotation
uniprot_id_map	Map UniProt IDs to Other Identifiers
workIn	Perform Operations in a Specified Directory and Return to the Original Directory