Package: scRNAstat 0.1.1

scRNAstat: A Pipeline to Process Single Cell RNAseq Data

A pipeline that can process single or multiple Single Cell RNAseq samples primarily specializes in Clustering and Dimensionality Reduction. Meanwhile we use common cell type marker genes for T cells, B cells, Myeloid cells, Epithelial cells, and stromal cells (Fiboblast, Endothelial cells, Pericyte, Smooth muscle cells) to visualize the Seurat clusters, to facilitate labeling them by biological names. Once users named each cluster, they can evaluate the quality of them again and find the de novo marker genes also.

Authors:Jianming Zeng [aut], Yonghe Xia [ctb, cre], Biotrainee group [cph, fnd]

scRNAstat_0.1.1.tar.gz
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scRNAstat_0.1.1.tgz(r-4.4-any)scRNAstat_0.1.1.tgz(r-4.3-any)
scRNAstat_0.1.1.tar.gz(r-4.5-noble)scRNAstat_0.1.1.tar.gz(r-4.4-noble)
scRNAstat_0.1.1.tgz(r-4.4-emscripten)
scRNAstat.pdf |scRNAstat.html
scRNAstat/json (API)

# Install 'scRNAstat' in R:
install.packages('scRNAstat', repos = c('https://xiayh17.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 2 scripts 193 downloads 6 exports 156 dependencies

Last updated 3 years agofrom:5baba4055e. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 17 2024
R-4.5-winWARNINGOct 17 2024
R-4.5-linuxWARNINGOct 17 2024
R-4.4-winWARNINGOct 17 2024
R-4.4-macWARNINGOct 17 2024
R-4.3-winWARNINGOct 17 2024
R-4.3-macWARNINGOct 17 2024

Exports:%>%basic_filterbasic_find_markersbasic_markersbasic_qcbasic_workflow

Dependencies:abindaskpassbackportsbase64encBHbitopsbslibcachemcaToolscheckmatecliclusterclustreecodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggforceggplot2ggraphggrepelggridgesglobalsgluegoftestgplotsgraphlayoutsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsyssystemfontstensortibbletidygraphtidyrtidyselecttinytextweenrutf8uwotvctrsviridisviridisLitewithrxfunxtableyamlzoo