# Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

## Documentation for package ‘easybio’ version 1.2.2

- 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