Package: scAnnotate 0.3

scAnnotate: An Automated Cell Type Annotation Tool for Single-Cell RNA-Sequencing Data

An entirely data-driven cell type annotation tools, which requires training data to learn the classifier, but not biological knowledge to make subjective decisions. It consists of three steps: preprocessing training and test data, model fitting on training data, and cell classification on test data. See Xiangling Ji,Danielle Tsao, Kailun Bai, Min Tsao, Li Xing, Xuekui Zhang.(2022)<doi:10.1101/2022.02.19.481159> for more details.

Authors:Xiangling Ji [aut], Danielle Tsao [aut], Kailun Bai [ctb], Min Tsao [aut], Li Xing [aut], Xuekui Zhang [aut, cre]

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scAnnotate.pdf |scAnnotate.html
scAnnotate/json (API)
NEWS

# Install 'scAnnotate' in R:
install.packages('scAnnotate', repos = c('https://ubcxzhang.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.

2.00 score 4 scripts 206 downloads 2 exports 152 dependencies

Last updated 8 months agofrom:df9145d8a8. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winOKNov 09 2024
R-4.5-linuxOKNov 09 2024
R-4.4-winOKNov 09 2024
R-4.4-macOKNov 09 2024
R-4.3-winOKNov 09 2024
R-4.3-macOKNov 09 2024

Exports:eva_calscAnnotate

Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachfsfuturefuture.applygenericsggplot2ggrepelggridgesglmnetglobalsgluegoftestgplotsgridExtragtablegtoolsharmonyherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulateRhpcBLASctlrlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshapeshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

Introduction

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2024-03-14
Started: 2022-07-01

Readme and manuals

Help Manual

Help pageTopics
eva_caleva_cal
pbmc1pbmc1
pbmc2pbmc2
predict_labelpredict_label
scAnnotatescAnnotate