Package: DR.SC 3.4

Wei Liu

DR.SC: Joint Dimension Reduction and Spatial Clustering

Joint dimension reduction and spatial clustering is conducted for Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.

Authors:Wei Liu [aut, cre], Yi Yang [aut], Jin Liu [aut]

DR.SC_3.4.tar.gz
DR.SC_3.4.zip(r-4.5)DR.SC_3.4.zip(r-4.4)DR.SC_3.4.zip(r-4.3)
DR.SC_3.4.tgz(r-4.4-x86_64)DR.SC_3.4.tgz(r-4.4-arm64)DR.SC_3.4.tgz(r-4.3-x86_64)DR.SC_3.4.tgz(r-4.3-arm64)
DR.SC_3.4.tar.gz(r-4.5-noble)DR.SC_3.4.tar.gz(r-4.4-noble)
DR.SC_3.4.tgz(r-4.4-emscripten)
DR.SC.pdf |DR.SC.html✨
DR.SC/json (API)

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

Peer review:

Bug tracker:https://github.com/feiyoung/dr.sc/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • dlpfc151510 - A human dorsolateral prefrontal cortex data

On CRAN:

dimension-reductionselfsupervisedspatial-clusteringspatial-transcriptomics

15 exports 5 stars 1.41 score 151 dependencies 1 dependents 29 scripts 417 downloads

Last updated 6 months agofrom:64d95135ab. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 17 2024
R-4.5-win-x86_64NOTESep 17 2024
R-4.5-linux-x86_64NOTESep 17 2024
R-4.4-win-x86_64OKSep 17 2024
R-4.4-mac-x86_64OKSep 17 2024
R-4.4-mac-aarch64OKSep 17 2024
R-4.3-win-x86_64OKSep 17 2024
R-4.3-mac-x86_64OKSep 17 2024
R-4.3-mac-aarch64OKSep 17 2024

Exports:DR.SCDR.SC_fitdrscPlotFindSVGsgendata_RNAExpgetAdjgetAdj_autogetAdj_manualmbicPlotread10XVisiumreadscRNAseqRunWPCAselectModelspatialPlotClusterstopSVGs

Dependencies:abindaskpassbase64encBHBiocGenericsbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkCompQuadFormcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesGiRaFglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmclustmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS4VectorssassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

DR-SC: installation

Rendered fromDR-SC.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2022-02-24
Started: 2021-11-24

DR-SC: DLPFC Data Analysis

Wei Liu

Rendered fromDR.SC.DLPFC.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2024-03-21
Started: 2022-07-31

DR-SC: simulation

Wei Liu

Rendered fromDR.SC.Simu.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2024-03-21
Started: 2021-10-05