Package: easybio 1.1.0

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]

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easybio.pdf |easybio.html✨
easybio/json (API)
NEWS

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

Peer review:

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:

limmageoqueryedgerfgseabioinformaticscellmarker2gsearna-seqsingle-cell

5.94 score 4 stars 24 scripts 288 downloads 33 exports 38 dependencies

Last updated 2 months agofrom:03a3d1b962. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-winOKNov 07 2024
R-4.5-linuxOKNov 07 2024
R-4.4-winOKNov 07 2024
R-4.4-macOKNov 07 2024
R-4.3-winOKNov 07 2024
R-4.3-macOKNov 07 2024

Exports:Artistavailable_tissue_classavailable_tissue_typecheck_markerdgeListdprocess_dgeListfinsertget_attrget_markergroupStatgroupStatIlimmaFitlist2dtlist2graphmatchCellMarker2plotEnrichment2plotGSEAplotMarkerDistributionplotORAplotPossibleCellplotRankplotSeuratDotplotVolcanoprepare_geoprepare_tcgasetcolnamessetrownamessetSavedirsplit_matrixtheme_publicationtuneParametersuniprot_id_mapworkIn

Dependencies:askpassclicolorspacecurldata.tablefansifarverggplot2gluegtablehttr2isobandlabelinglatticelifecyclelimmamagrittrMASSMatrixmgcvmunsellnlmeopensslpillarpkgconfigR6rappdirsRColorBrewerrlangscalesstatmodsystibbleutf8vctrsviridisLitewithrxml2

Example Workflow for Bulk RNA-Seq Analysis

Rendered fromexample-bulk-rna-seq-workflow.Rmdusingknitr::rmarkdownon Nov 07 2024.

Last update: 2024-09-16
Started: 2024-09-02

Example Workflow for Single Cell Annotation Using CellMarker2.0

Rendered fromexample-single-cell-annotation.Rmdusingknitr::rmarkdownon Nov 07 2024.

Last update: 2024-09-16
Started: 2024-09-02

Readme and manuals

Help Manual

Help pageTopics
Visualization Artist for Custom PlotsArtist
Retrieve Available Tissue Classes for a Given Speciesavailable_tissue_class
Retrieve Available Tissue Types for a Given Speciesavailable_tissue_type
Verify Markers for Specific Clusters Using matchCellMarkercheck_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
Insert Specific Values into a Character Vector at Defined Positionsfinsert
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 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
Match Markers with cellMarker2 DatasetmatchCellMarker2
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 Dot Plots for Markers from check_markerplotSeuratDot
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 Submatrices by Columnsplit_matrix
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