Package: easybio 1.3.0

Wei Cui

easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker 3.0' database <https://bio-bigdata.hrbmu.edu.cn/CellMarker/>. Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGA<https://portal.gdc.cancer.gov/> and GEO<https://www.ncbi.nlm.nih.gov/geo/> datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows. See Wei Cui (2024) <doi:10.1101/2024.09.14.609619> for more details.

Authors:Wei Cui [aut, cre, cph]

easybio_1.3.0.tar.gz
easybio_1.3.0.zip(r-4.7-any)easybio_1.3.0.zip(r-4.6-any)
easybio_1.3.0.tar.gz(r-4.7-any)easybio_1.3.0.tar.gz(r-4.6-any)
easybio_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
easybio/json (API)

# Install 'easybio' in R:
install.packages('easybio', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/person-c/easybio/issues

Datasets:
  • CHOL_DEGs - Example DEGs data from Limma-Voom workflow for TCGA-CHOL project
  • pbmc.markers - Example marker data from Seurat::FindAllMarkers

On CRAN:

Conda:

limmageoqueryedgerfgsea

3.86 score 1 stars 48 scripts 485 downloads 54 exports 27 dependencies

Last updated from:6010abbdbc. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develOK229
source / vignettesOK272
linux-releaseOK504
windows-develOK168
windows-releaseOK182
wasm-releaseOK178

Exports:Artistavailable_eleavailable_tissue_classavailable_tissue_typecheck_markerdge_listdgeListdprocess_dgeListfinsertget_attrget_markergroup_statgroup_stat_igroupStatgroupStatIlimma_fitlimmaFitlist2dtlist2graphmatch_refmatchCellMarker2plot_enrichmentplot_gseaplot_marker_distributionplot_oraplot_possible_cellplot_rankplot_seurat_dotplot_volcanoplotEnrichment2plotGSEAplotMarkerDistributionplotORAplotPossibleCellplotRankplotSeuratDotplotVolcanoprepare_geoprepare_tcgaprocess_dge_listset_colnamesset_rownamesset_savedirsetcolnamessetrownamessetSavedirsplit_matrixsuggest_best_matchtheme_publicationtune_parameterstuneParametersuniprot_id_mapwork_inworkIn

Dependencies:askpassbackportscheckmateclicpp11curldata.tablefarverggplot2gluegtablehttr2isobandlabelinglifecyclemagrittropensslR6RColorBrewerrlangS7scalessysvctrsviridisLitewithrxml2

Example Workflow for Bulk RNA-seq Analysis with limma-voom
Limma-voom workflow | Prepare data | Example Workflow: TCGA CHOL Project
Rendered fromexample_limma.Rmdusinglitedown::vignette

Last update: 2026-10-07
Started: 2025-08-30

Example Workflow for Single-Cell Annotation with easybio
Introduction | Setup | Step 1: Automated Annotation with match_ref | Bounding the search to the right tissue | Step 2: Verification and Exploration | Answering "Why was this annotation made?" | Answering "Is this annotation correct?" | Visual Confirmation with plot_seurat_dot | Step 3: Final Manual Curation | Using a Custom Marker Database | Additional Utilities | get_marker() | plot_marker_distribution()
Rendered fromexample-sc-seq-workflow.Rmdusinglitedown::vignette

Last update: 2026-10-07
Started: 2025-08-30

Exploratory Data Visualization with the Artist Class
Introduction | Setup | Basic Usage | Statistical Tests and Auto-Annotation | Method Chaining | Data Transformation with fun | Available Plot Types | Dumbbell Plot | Bubble Plot | Divergence Bar Chart | Lollipop Plot | Contour Plot | Scatter Plot with Ellipses | Donut Plot | Pie Chart | Reviewing Your Exploration History | Summary
Rendered fromexample-artist.Rmdusinglitedown::vignette

Last update: 2026-10-07
Started: 2026-10-07

Readme and manuals

Help Manual

Help pageTopics
Visualization Artist for Custom PlotsArtist
Extract Unique Elements from a Column with Optional Filteringavailable_ele
Retrieve Available Tissue Classes for a Given Speciesavailable_tissue_class
Retrieve Available Tissue Types for a Given Speciesavailable_tissue_type
Verify and Explore Cell Type Annotationscheck_marker
Example DEGs data from Limma-Voom workflow for TCGA-CHOL projectCHOL_DEGs
Construct a DGEList Objectdge_list
Construct a DGEList Object (Deprecated)dgeList
Filter and Normalize DGEList Data (Deprecated)dprocess_dgeList
Create a Vector from an Index-to-Label Mapfinsert
Retrieve Attributes from an R Objectget_attr
Retrieve Markers for Specific Cells from cellMarker3get_marker
Perform Summary Analysis by Group Using Regular Expressionsgroup_stat
Perform Summary Analysis by Group Using an column Indexgroup_stat_i
Summarize Data by Group Using Regular Expressions (Deprecated)groupStat
Summarize Data by Group Using an Index (Deprecated)groupStatI
Fit a Linear Model for RNA-seq data using limmalimma_fit
Fit a Linear Model for RNA-seq Data (Deprecated)limmaFit
Convert a List with Vector Values to a Long Data.tablelist2dt
Convert a Named List into a Graph Based on Overlaplist2graph
Annotate Clusters by Matching Markers with the CellMarker 3.0 Databasematch_ref
Annotate Clusters by Matching Markers (Deprecated)matchCellMarker2
Example marker data from Seurat::FindAllMarkers()pbmc.markers
Plot Enrichment for a Specific Pathway in fgseaplot_enrichment
Visualization of GSEA Result from 'fgsea::fgsea()'plot_gsea
Plot Distribution of a Marker Across Tissues and Cell Typesplot_marker_distribution
Visualization of ORA Test Resultsplot_ora
Plot Possible Cell Distribution Based on match_ref() Resultsplot_possible_cell
Visualization of GSEA Rank Statisticsplot_rank
Create a Dot Plot to Visualize Marker Gene Expressionplot_seurat_dot
Plot Volcano Plot for Differentially Expressed Genesplot_volcano
Plot Enrichment for a Pathway (Deprecated)plotEnrichment2
Visualize GSEA Results (Deprecated)plotGSEA
Plot Distribution of a Marker (Deprecated)plotMarkerDistribution
Visualize ORA Test Results (Deprecated)plotORA
Plot Possible Cell Distribution (Deprecated)plotPossibleCell
Visualize GSEA Rank Statistics (Deprecated)plotRank
Create a Dot Plot of Marker Gene Expression (Deprecated)plotSeuratDot
Plot a Volcano Plot (Deprecated)plotVolcano
Download and Process GEO Dataprepare_geo
Prepare TCGA Data for Analysisprepare_tcga
Filter Low-Expressed Genes and Normalize DGEList Dataprocess_dge_list
Rename Column Names of a Data Frame or Matrixset_colnames
Rename Row Names of a Data Frame or Matrixset_rownames
Set a Directory for Saving Filesset_savedir
Rename Column Names (Deprecated)setcolnames
Rename Row Names (Deprecated)setrownames
Set a Directory for Saving Files (Deprecated)setSavedir
Split a Matrix into Smaller Sub-matrices by Column or Rowsplit_matrix
Suggest Best Matches for a String from a Vector of Choicessuggest_best_match
Custom ggplot2 Theme for Academic Publicationstheme_publication
Optimize Resolution and Gene Number Parameters for Cell Type Annotationtune_parameters
Tune Parameters for Cell Type Annotation (Deprecated)tuneParameters
Map UniProt IDs to Other Identifiersuniprot_id_map
Perform Operations in a Specified Directory and Return to the Original Directorywork_in
Perform Operations in a Directory (Deprecated)workIn