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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。

Stay up-to-date

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

447

Version

1.2.3

License

MIT + file LICENSE

Issues

0

Pull Requests

1

Stars

12

Forks

1

Maintainer

Wei Cui

Last Published

October 2nd, 2025

Functions in easybio (1.2.3)

list2graph

Convert a Named List into a Graph Based on Overlap
get_marker

Retrieve Markers for Specific Cells from cellMarker2
get_attr

Retrieve Attributes from an R Object
list2dt

Convert a List with Vector Values to a Long Data.table
matchCellMarker2

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

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

Prepare TCGA Data for Analysis
groupStat

Perform Summary Analysis by Group Using Regular Expressions
plotRank

Visualization of GSEA Rank Statistics
plotSeuratDot

Create a Dot Plot to Visualize Marker Gene Expression
setSavedir

Set a Directory for Saving Files
setrownames

Rename Row Names of a Data Frame or Matrix
setcolnames

Rename Column Names of a Data Frame or Matrix
theme_publication

Custom ggplot2 Theme for Academic Publications
tuneParameters

Optimize Resolution and Gene Number Parameters for Cell Type Annotation
plotMarkerDistribution

Plot Distribution of a Marker Across Tissues and Cell Types
workIn

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

Plot Possible Cell Distribution Based on matchCellMarker2() Results
uniprot_id_map

Map UniProt IDs to Other Identifiers
prepare_geo

Download and Process GEO Data
groupStatI

Perform Summary Analysis by Group Using an column Index
split_matrix

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

Plot Volcano Plot for Differentially Expressed Genes
plotORA

Visualization of ORA Test Results
suggest_best_match

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

Construct a DGEList Object
dprocess_dgeList

Filter Low-Expressed Genes and Normalize DGEList Data
check_marker

Verify and Explore Cell Type Annotations
available_ele

Extract Unique Elements from a Column with Optional Filtering
finsert

Create a Vector from an Index-to-Label Map
available_tissue_class

Retrieve Available Tissue Classes for a Given Species
available_tissue_type

Retrieve Available Tissue Types for a Given Species
easybio-package

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

Visualization Artist for Custom Plots
CHOL_DEGs

Example DEGs data from Limma-Voom workflow for TCGA-CHOL project
plotEnrichment2

Plot Enrichment for a Specific Pathway in fgsea
pbmc.markers

Example marker data from Seurat::FindAllMarkers()
plotGSEA

Visualization of GSEA Result from fgsea::fgsea()