Files in quadbiolab/Pando
Inferring regulomes from multi-modal single-cell genomics data
.Rbuildignore
.github/workflows/check-build.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
Pando.Rproj
R/generics.R
R/grn.R
R/models.R
R/objects.R
R/plots.R
R/regions.R
R/utils.R
README.md
data/EnsDb.Hsapiens.v93.annot.UCSC.hg38.RData
data/SCREEN.ccRE.UCSC.hg38.RData
data/motif2tf.RData
data/motifs.RData
data/phastConsElements20Mammals.UCSC.hg38.RData
docs/404.html
docs/LICENSE-text.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/advanced.html
docs/articles/advanced_files/header-attrs-2.8/header-attrs.js
docs/articles/association.html
docs/articles/association_files/header-attrs-2.8/header-attrs.js
docs/articles/getting_started.html
docs/articles/getting_started_files/figure-html/unnamed-chunk-22-1.png
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docs/articles/getting_started_files/header-attrs-2.8/header-attrs.js
docs/articles/index.html
docs/articles/models.html
docs/articles/models_files/header-attrs-2.8/header-attrs.js
docs/articles/regions.html
docs/articles/regions_files/header-attrs-2.8/header-attrs.js
docs/articles/visualization.html
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docs/articles/visualization_files/figure-html/unnamed-chunk-8-1.png
docs/articles/visualization_files/header-attrs-2.8/header-attrs.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/DefaultNetwork.html
docs/reference/GetAssaySummary.html
docs/reference/GetGRN.html
docs/reference/GetNetwork.html
docs/reference/GetNetworkData.html
docs/reference/Network-class.html
docs/reference/NetworkFeatures.html
docs/reference/NetworkGraph.html
docs/reference/NetworkModules.html
docs/reference/NetworkParams.html
docs/reference/NetworkRegions.html
docs/reference/NetworkTFs.html
docs/reference/Params.html
docs/reference/Regions-class.html
docs/reference/RegulatoryNetwork-class.html
docs/reference/Rplot001.png
docs/reference/SeuratPlus-class.html
docs/reference/ae.html
docs/reference/aggregate_assay.html
docs/reference/aggregate_matrix.html
docs/reference/coef.html
docs/reference/compute_metrics.html
docs/reference/cv_folds.html
docs/reference/figures/logo.png
docs/reference/find_modules.html
docs/reference/find_motifs.html
docs/reference/find_peaks_near_genes.html
docs/reference/fit_bagging_ridge.html
docs/reference/fit_bayesian_ridge.html
docs/reference/fit_brms.html
docs/reference/fit_cvglmnet.html
docs/reference/fit_glm.html
docs/reference/fit_glmnet.html
docs/reference/fit_grn_models.html
docs/reference/fit_model.html
docs/reference/fit_xgb.html
docs/reference/format_coefs.html
docs/reference/get_network_graph.html
docs/reference/get_tf_network.html
docs/reference/get_umap.html
docs/reference/gof.html
docs/reference/hello.html
docs/reference/index.html
docs/reference/infer_grn.html
docs/reference/initiate_grn.html
docs/reference/log_message.html
docs/reference/mae.html
docs/reference/map_par.html
docs/reference/mape.html
docs/reference/mse.html
docs/reference/no_legend.html
docs/reference/no_margin.html
docs/reference/no_x_text.html
docs/reference/no_y_text.html
docs/reference/plot_gof.html
docs/reference/plot_module_metrics.html
docs/reference/plot_network_graph.html
docs/reference/plot_tf_network.html
docs/reference/print.html
docs/reference/r2.html
docs/reference/rmse.html
docs/reference/rse.html
docs/reference/scale_axis_rangeframe.html
docs/reference/sparse_cor.html
docs/reference/sparse_covcor.html
docs/reference/sse.html
docs/reference/theme_rangeframe.html
index.md
man/DefaultNetwork.Rd
man/GRNData-class.Rd
man/GetAssay.Rd
man/GetAssaySummary.Rd
man/GetGRN.Rd
man/GetNetwork.Rd
man/LayerData.Rd
man/Network-class.Rd
man/NetworkFeatures.Rd
man/NetworkGraph.Rd
man/NetworkModules.Rd
man/NetworkParams.Rd
man/NetworkRegions.Rd
man/NetworkTFs.Rd
man/Params.Rd
man/Regions-class.Rd
man/RegulatoryNetwork-class.Rd
man/VariableFeatures.Rd
man/aggregate_assay.Rd
man/aggregate_matrix.Rd
man/coef.Rd
man/create_GRNData.Rd
man/dMcast.Rd
man/fast_aggregate.Rd
man/figures/logo.png
man/find_modules.Rd
man/find_motifs.Rd
man/find_peaks_near_genes.Rd
man/fit_bagging_ridge.Rd
man/fit_bayesian_ridge.Rd
man/fit_brms.Rd
man/fit_cvglmnet.Rd
man/fit_glm.Rd
man/fit_glmnet.Rd
man/fit_grn_models.Rd
man/fit_model.Rd
man/fit_xgb.Rd
man/format_coefs.Rd
man/get_network_graph.Rd
man/get_tf_network.Rd
man/get_umap.Rd
man/gof.Rd
man/hello.Rd
man/infer_grn.Rd
man/initiate_grn.Rd
man/log_message.Rd
man/map_par.Rd
man/no_legend.Rd
man/no_margin.Rd
man/no_x_text.Rd
man/no_y_text.Rd
man/plot_gof.Rd
man/plot_module_metrics.Rd
man/plot_network_graph.Rd
man/plot_tf_network.Rd
man/print.Rd
man/r2.Rd
man/rse.Rd
man/sparse_cor.Rd
man/sparse_covcor.Rd
man/sse.Rd
pkgdown/_pkgdown.yml
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/test_manual.R
tests/testthat/test_core.R
tests/testthat/test_utils.R
vignettes/advanced.Rmd
vignettes/association.Rmd
vignettes/getting_started.Rmd
vignettes/models.Rmd
vignettes/regions.Rmd
vignettes/visualization.Rmd
