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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.

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

309

Version

1.1.1

License

MIT + file LICENSE

Issues

0

Pull Requests

0

Stars

11

Forks

0

Maintainer

Wei Cui

Last Published

February 12th, 2025

Functions in easybio (1.1.1)

pbmc.markers

Example marker data from Seurat::FindAllMarkers()
limmaFit

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

Visualization of GSEA Rank Statistics
plotSeuratDot

Create Dot Plots for Markers from check_marker
plotEnrichment2

Plot Enrichment for a Specific Pathway in fgsea
list2dt

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

Perform Summary Analysis by Group Using Regular Expressions
plotORA

Visualization of ORA Test Results
prepare_tcga

Prepare TCGA Data for Analysis
setSavedir

Set a Directory for Saving Files
plotPossibleCell

Plot Possible Cell Distribution Based on matchCellMarker2() Results
tuneParameters

Optimize Resolution and Gene Number Parameters for Cell Type Annotation
uniprot_id_map

Map UniProt IDs to Other Identifiers
setcolnames

Rename Column Names of a Data Frame or Matrix
plotGSEA

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

Rename Row Names of a Data Frame or Matrix
plotMarkerDistribution

Plot Distribution of a Marker Across Tissues and Cell Types
groupStatI

Perform Summary Analysis by Group Using an column Index
workIn

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

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

Custom ggplot2 Theme for Academic Publications
plotVolcano

Plot Volcano Plot for Differentially Expressed Genes
prepare_geo

Download and Process GEO Data
available_tissue_class

Retrieve Available Tissue Classes for a Given Species
CHOL_DEGs

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

Visualization Artist for Custom Plots
dprocess_dgeList

Filter Low-Expressed Genes and Normalize DGEList Data
finsert

Insert Specific Values into a Character Vector at Defined Positions
get_attr

Retrieve Attributes from an R Object
get_marker

Retrieve Markers for Specific Cells from cellMarker2
available_tissue_type

Retrieve Available Tissue Types for a Given Species
check_marker

Verify Markers for Specific Clusters Using matchCellMarker
dgeList

Construct a DGEList Object
list2graph

Convert a Named List into a Graph Based on Overlap
matchCellMarker2

Match Markers with cellMarker2 Dataset