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easybio

Installation and Usage

install.packages("easybio", repos = c("https://person-c.r-universe.dev", "https://cloud.r-project.org"))

To know how to use this package to do single cell annotation, see the article.

参考这个视频

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To learn the difference between development version and CRAN version, see NEWS.

Citation

If you use the single-cell annotation functionality from easybio, consider citing:

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Version

Install

install.packages('easybio')

Monthly Downloads

297

Version

1.2.2

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Wei Cui

Last Published

September 1st, 2025

Functions in easybio (1.2.2)

plotEnrichment2

Plot Enrichment for a Specific Pathway in fgsea
get_attr

Retrieve Attributes from an R Object
groupStat

Perform Summary Analysis by Group Using Regular Expressions
limmaFit

Fit a Linear Model for RNA-seq data using limma
list2graph

Convert a Named List into a Graph Based on Overlap
groupStatI

Perform Summary Analysis by Group Using an column Index
pbmc.markers

Example marker data from Seurat::FindAllMarkers()
matchCellMarker2

Annotate Clusters by Matching Markers with the CellMarker2.0 Database
get_marker

Retrieve Markers for Specific Cells from cellMarker2
list2dt

Convert a List with Vector Values to a Long Data.table
plotRank

Visualization of GSEA Rank Statistics
plotPossibleCell

Plot Possible Cell Distribution Based on matchCellMarker2() Results
plotMarkerDistribution

Plot Distribution of a Marker Across Tissues and Cell Types
plotSeuratDot

Create a Dot Plot to Visualize Marker Gene Expression
prepare_tcga

Prepare TCGA Data for Analysis
setSavedir

Set a Directory for Saving Files
plotORA

Visualization of ORA Test Results
plotVolcano

Plot Volcano Plot for Differentially Expressed Genes
plotGSEA

Visualization of GSEA Result from fgsea::fgsea()
prepare_geo

Download and Process GEO Data
uniprot_id_map

Map UniProt IDs to Other Identifiers
workIn

Perform Operations in a Specified Directory and Return to the Original Directory
tuneParameters

Optimize Resolution and Gene Number Parameters for Cell Type Annotation
theme_publication

Custom ggplot2 Theme for Academic Publications
suggest_best_match

Suggest Best Matches for a String from a Vector of Choices
split_matrix

Split a Matrix into Smaller Sub-matrices by Column or Row
setrownames

Rename Row Names of a Data Frame or Matrix
setcolnames

Rename Column Names of a Data Frame or Matrix
available_tissue_type

Retrieve Available Tissue Types for a Given Species
check_marker

Verify and Explore Cell Type Annotations
available_ele

Extract Unique Elements from a Column with Optional Filtering
easybio-package

easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit
available_tissue_class

Retrieve Available Tissue Classes for a Given Species
CHOL_DEGs

Example DEGs data from Limma-Voom workflow for TCGA-CHOL project
dprocess_dgeList

Filter Low-Expressed Genes and Normalize DGEList Data
dgeList

Construct a DGEList Object
Artist

Visualization Artist for Custom Plots
finsert

Create a Vector from an Index-to-Label Map