Files in plantformatics/Socrates
Analysis of scATAC-seq data
.DS_Store
.Rbuildignore
._.DS_Store
.gitignore
DESCRIPTION
NAMESPACE
R/._cluster.R
R/._doublet_analysis.R
R/._models.R
R/._quality_control.R
R/._reduce_dimensions.R
R/._visualizations.R
R/cluster.R
R/coaccessibility.R
R/doublet_analysis.R
R/merge_soc_objects.R
R/models.R
R/preprocessing.R
R/quality_control.R
R/reduce_dimensions.R
R/visualizations.R
README.md
Socrates.Rproj
data/obj.rda
data/scATAC_5K_pbmc.rds
inst/extdata/gencode.v19.annotation.gff3.gz
inst/extdata/hg19.txt
inst/extdata/pbmc_atac_10x.1.5K_cells.metadata.txt
inst/extdata/pbmc_atac_10x.1.5K_cells.sparse.gz
inst/extdata/test.tn5.bed.gz
man/buildMetaData_OG.Rd
man/callACRs.Rd
man/callClusters.Rd
man/cleanData.Rd
man/coAccess.Rd
man/convertSparseData.Rd
man/countRemoveOrganelle.Rd
man/detectDoublets.Rd
man/filtDistClst.Rd
man/filterDoublets.Rd
man/filterSingle.Rd
man/findCells_OG.Rd
man/generateMatrix.Rd
man/getFDR.Rd
man/isCell.Rd
man/loadBEDandGenomeData.Rd
man/loadSparseData.Rd
man/logisticModel.Rd
man/mergeQCdataRDS.Rd
man/mergeSocratesRDS.Rd
man/plotUMAP.Rd
man/projectUMAP.Rd
man/reduceDims.Rd
man/regModel.Rd
man/regModel2.Rd
man/runCicero.Rd
man/standardizeResiduals.Rd
man/tfidf.Rd
man/writeReadME.Rd
tutorial_figures/Socrates_home_image.png
tutorial_figures/plotClusters-1.png
tutorial_figures/plotClusters-2.png
tutorial_figures/plotUMAPraw-1.png
tutorial_figures/plotUMAPraw-2.png
tutorial_figures/unnamed-chunk-11-1.png
tutorial_figures/unnamed-chunk-9-1.png
tutorial_figures/view_distributions-1.png
tutorial_figures/view_distributions-2.png
vignettes/Load_and_QC_data.Rmd
vignettes/Load_and_QC_data.html
vignettes/Socrates_clustering_comparison_tutorial.html
vignettes/Socrates_clustering_comparison_tutorial.md
vignettes/Socrates_clustering_comparison_tutorial_html.Rmd
vignettes/Socrates_clustering_comparison_tutorial_html.html
vignettes/Socrates_coACRs_tutorial.Rmd
vignettes/Socrates_coACRs_tutorial.html
vignettes/Socrates_simple_clustering_tutorial.Rmd
vignettes/Socrates_simple_clustering_tutorial.html
vignettes/Socrates_simple_clustering_tutorial.md
