Package: easybio 1.2.3

Wei Cui

easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database (see Xia Li, Peng Wang, Yunpeng Zhang (2023) <doi:10.1093/nar/gkac947>). 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_1.2.3.tar.gz
easybio_1.2.3.tar.gz(r-4.7-any)easybio_1.2.3.tar.gz(r-4.6-any)
easybio_1.2.3.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

4.16 score 1 stars 48 scripts 384 downloads 35 exports 28 dependencies

Last updated from:599577890e. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK208
source / vignettesOK286
linux-release-x86_64OK222
wasm-releaseOK184

Exports:Artistavailable_eleavailable_tissue_classavailable_tissue_typecheck_markerdgeListdprocess_dgeListfinsertget_attrget_markergroupStatgroupStatIlimmaFitlist2dtlist2graphmatchCellMarker2plotEnrichment2plotGSEAplotMarkerDistributionplotORAplotPossibleCellplotRankplotSeuratDotplotVolcanoprepare_geoprepare_tcgasetcolnamessetrownamessetSavedirsplit_matrixsuggest_best_matchtheme_publicationtuneParametersuniprot_id_mapworkIn

Dependencies:askpassbackportscheckmateclicpp11curldata.tablefarverggplot2gluegtablehttr2isobandlabelinglifecyclemagrittropensslR6rappdirsRColorBrewerrlangS7scalessysvctrsviridisLitewithrxml2

Example Workflow for Single-Cell Annotation with easybio
Introduction | Setup | Step 1: Automated Annotation with matchCellMarker2 | Step 2: Verification and Exploration | Answering "Why was this annotation made?" | Answering "Is this annotation correct?" | Visual Confirmation with plotSeuratDot | Step 3: Final Manual Curation | Using a Custom Marker Database | Additional Utilities | get_marker() | plotMarkerDistribution()
Rendered fromexample-sc-seq-workflow.Rmdusinglitedown::vignette

Last update: 2025-10-02
Started: 2025-08-30

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: 2025-08-30
Started: 2025-08-30

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 ObjectdgeList
Filter Low-Expressed Genes and Normalize DGEList Datadprocess_dgeList
Create a Vector from an Index-to-Label Mapfinsert
Retrieve Attributes from an R Objectget_attr
Retrieve Markers for Specific Cells from cellMarker2get_marker
Perform Summary Analysis by Group Using Regular ExpressionsgroupStat
Perform Summary Analysis by Group Using an column IndexgroupStatI
Fit a Linear Model for RNA-seq data using limmalimmaFit
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 CellMarker2.0 DatabasematchCellMarker2
Example marker data from Seurat::FindAllMarkers()pbmc.markers
Plot Enrichment for a Specific Pathway in fgseaplotEnrichment2
Visualization of GSEA Result from 'fgsea::fgsea()'plotGSEA
Plot Distribution of a Marker Across Tissues and Cell TypesplotMarkerDistribution
Visualization of ORA Test ResultsplotORA
Plot Possible Cell Distribution Based on matchCellMarker2() ResultsplotPossibleCell
Visualization of GSEA Rank StatisticsplotRank
Create a Dot Plot to Visualize Marker Gene ExpressionplotSeuratDot
Plot Volcano Plot for Differentially Expressed GenesplotVolcano
Download and Process GEO Dataprepare_geo
Prepare TCGA Data for Analysisprepare_tcga
Rename Column Names of a Data Frame or Matrixsetcolnames
Rename Row Names of a Data Frame or Matrixsetrownames
Set a Directory for Saving FilessetSavedir
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 AnnotationtuneParameters
Map UniProt IDs to Other Identifiersuniprot_id_map
Perform Operations in a Specified Directory and Return to the Original DirectoryworkIn