├── .Rhistory ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── PISCES.Rproj ├── R ├── aracne_funcs.R ├── cluster_funcs.R ├── gexp-transform_funcs.R ├── human-regulators-data.R ├── mouse-regulators-data.R ├── mr_funcs.R ├── mt-genes-data.R ├── mwkmeans_funcs.R ├── narnea_funcs.R ├── object_funcs.R ├── pbmc-raw-data.R ├── plotting_funcs.R ├── reduction_funcs.R ├── util_funcs.R └── viper_funcs.R ├── README.md ├── data ├── ARACNe.zip ├── PBMC.raw.rda ├── human_regulators.rda ├── mouse_regulators.rda └── mt_genes.rda ├── inst └── extdata │ ├── abt_map.rda │ ├── cbmc_abt.rda │ ├── cbmc_networks.rda │ └── cbmc_rna.rda ├── man ├── ARACNeTable.Rd ├── AddDist.Rd ├── AddGES.Rd ├── AddMDS.Rd ├── AddNetworks.Rd ├── AddPCA.Rd ├── AddPISCESAssay.Rd ├── AddUMAP.Rd ├── KNN.Rd ├── LouvainClust.Rd ├── MWKMeans.Rd ├── MWUMrs.Rd ├── MinAssignments.Rd ├── MinClusters.Rd ├── NormalizeExpression.Rd ├── ObjectiveValue.Rd ├── PAMClust.Rd ├── PISCESActivity.Rd ├── PISCESViper.Rd ├── RegProcess.Rd ├── TwoMatVipSim.Rd ├── ViperMerge.Rd ├── WeightedVIPER.Rd ├── WriteMetaCells.Rd ├── cluster_mr_heatmap.Rd ├── cluster_mr_volcano.Rd ├── cluster_pair_mr_volcano.Rd ├── cluster_signature_mrs.Rd ├── cohen_kappa.Rd ├── color_levels.Rd ├── combine_nes.Rd ├── convert_genes.Rd ├── cor_dist.Rd ├── cpm_norm.Rd ├── directed_nes.Rd ├── ecdf_ges.Rd ├── ecdf_norm.Rd ├── fast_pca.Rd ├── figures │ ├── fig_abt-markers.jpg │ ├── fig_qc.jpg │ ├── fig_vip-clust.jpg │ ├── fig_vip-markers.jpg │ └── fig_vip-mrs.jpg ├── get_mr_set.Rd ├── group_colors.Rd ├── human_regulators.Rd ├── internal_ges.Rd ├── kappa_cluster_mrs.Rd ├── kw_cluster_mrs.Rd ├── log_kw.Rd ├── louvain_clust.Rd ├── louvain_k.Rd ├── make_mds.Rd ├── make_metacells.Rd ├── make_umap.Rd ├── matrix_convert_genes.Rd ├── matrix_narnea.Rd ├── meta_narnea.Rd ├── mouse_regulators.Rd ├── mt_genes.Rd ├── narnea_combine.Rd ├── nes_covariance.Rd ├── network_match_narnea.Rd ├── opt_kappa.Rd ├── pairwise_cluster_mrs.Rd ├── pam_k.Rd ├── pbmc.raw.Rd ├── pf_norm.Rd ├── pflpf_norm.Rd ├── qc_filt.Rd ├── qc_plot.Rd ├── quantile_breaks.Rd ├── read10X.Rd ├── scale_ges.Rd ├── sig_features.Rd ├── stouffer_cluster_mrs.Rd ├── stouffer_narnea.Rd ├── undirected_nes.Rd ├── unweighted_integration.Rd └── weighted_integration.Rd └── vignettes ├── .gitignore ├── general-workflow.Rmd └── pisces_pbmc.Rmd /.Rhistory: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/.Rhistory -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | inst/doc 2 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/NAMESPACE -------------------------------------------------------------------------------- /PISCES.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/PISCES.Rproj -------------------------------------------------------------------------------- /R/aracne_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/aracne_funcs.R -------------------------------------------------------------------------------- /R/cluster_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/cluster_funcs.R -------------------------------------------------------------------------------- /R/gexp-transform_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/gexp-transform_funcs.R -------------------------------------------------------------------------------- /R/human-regulators-data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/human-regulators-data.R -------------------------------------------------------------------------------- /R/mouse-regulators-data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/mouse-regulators-data.R -------------------------------------------------------------------------------- /R/mr_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/mr_funcs.R -------------------------------------------------------------------------------- /R/mt-genes-data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/mt-genes-data.R -------------------------------------------------------------------------------- /R/mwkmeans_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/mwkmeans_funcs.R -------------------------------------------------------------------------------- /R/narnea_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/narnea_funcs.R -------------------------------------------------------------------------------- /R/object_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/object_funcs.R -------------------------------------------------------------------------------- /R/pbmc-raw-data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/pbmc-raw-data.R -------------------------------------------------------------------------------- /R/plotting_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/plotting_funcs.R -------------------------------------------------------------------------------- /R/reduction_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/reduction_funcs.R -------------------------------------------------------------------------------- /R/util_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/util_funcs.R -------------------------------------------------------------------------------- /R/viper_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/R/viper_funcs.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/README.md -------------------------------------------------------------------------------- /data/ARACNe.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/data/ARACNe.zip -------------------------------------------------------------------------------- /data/PBMC.raw.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/data/PBMC.raw.rda -------------------------------------------------------------------------------- /data/human_regulators.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/data/human_regulators.rda -------------------------------------------------------------------------------- /data/mouse_regulators.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/data/mouse_regulators.rda -------------------------------------------------------------------------------- /data/mt_genes.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/data/mt_genes.rda -------------------------------------------------------------------------------- /inst/extdata/abt_map.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/inst/extdata/abt_map.rda -------------------------------------------------------------------------------- /inst/extdata/cbmc_abt.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/inst/extdata/cbmc_abt.rda -------------------------------------------------------------------------------- /inst/extdata/cbmc_networks.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/inst/extdata/cbmc_networks.rda -------------------------------------------------------------------------------- /inst/extdata/cbmc_rna.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/inst/extdata/cbmc_rna.rda -------------------------------------------------------------------------------- /man/ARACNeTable.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/ARACNeTable.Rd -------------------------------------------------------------------------------- /man/AddDist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/AddDist.Rd -------------------------------------------------------------------------------- /man/AddGES.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/AddGES.Rd -------------------------------------------------------------------------------- /man/AddMDS.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/AddMDS.Rd -------------------------------------------------------------------------------- /man/AddNetworks.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/AddNetworks.Rd -------------------------------------------------------------------------------- /man/AddPCA.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/AddPCA.Rd -------------------------------------------------------------------------------- /man/AddPISCESAssay.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/AddPISCESAssay.Rd -------------------------------------------------------------------------------- /man/AddUMAP.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/AddUMAP.Rd -------------------------------------------------------------------------------- /man/KNN.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/KNN.Rd -------------------------------------------------------------------------------- /man/LouvainClust.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/LouvainClust.Rd -------------------------------------------------------------------------------- /man/MWKMeans.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/MWKMeans.Rd -------------------------------------------------------------------------------- /man/MWUMrs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/MWUMrs.Rd -------------------------------------------------------------------------------- /man/MinAssignments.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/MinAssignments.Rd -------------------------------------------------------------------------------- /man/MinClusters.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/MinClusters.Rd -------------------------------------------------------------------------------- /man/NormalizeExpression.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/NormalizeExpression.Rd -------------------------------------------------------------------------------- /man/ObjectiveValue.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/ObjectiveValue.Rd -------------------------------------------------------------------------------- /man/PAMClust.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/PAMClust.Rd -------------------------------------------------------------------------------- /man/PISCESActivity.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/PISCESActivity.Rd -------------------------------------------------------------------------------- /man/PISCESViper.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/PISCESViper.Rd -------------------------------------------------------------------------------- /man/RegProcess.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/RegProcess.Rd -------------------------------------------------------------------------------- /man/TwoMatVipSim.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/TwoMatVipSim.Rd -------------------------------------------------------------------------------- /man/ViperMerge.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/ViperMerge.Rd -------------------------------------------------------------------------------- /man/WeightedVIPER.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/WeightedVIPER.Rd -------------------------------------------------------------------------------- /man/WriteMetaCells.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/WriteMetaCells.Rd -------------------------------------------------------------------------------- /man/cluster_mr_heatmap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/cluster_mr_heatmap.Rd -------------------------------------------------------------------------------- /man/cluster_mr_volcano.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/cluster_mr_volcano.Rd -------------------------------------------------------------------------------- /man/cluster_pair_mr_volcano.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/cluster_pair_mr_volcano.Rd -------------------------------------------------------------------------------- /man/cluster_signature_mrs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/cluster_signature_mrs.Rd -------------------------------------------------------------------------------- /man/cohen_kappa.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/cohen_kappa.Rd -------------------------------------------------------------------------------- /man/color_levels.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/color_levels.Rd -------------------------------------------------------------------------------- /man/combine_nes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/combine_nes.Rd -------------------------------------------------------------------------------- /man/convert_genes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/convert_genes.Rd -------------------------------------------------------------------------------- /man/cor_dist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/cor_dist.Rd -------------------------------------------------------------------------------- /man/cpm_norm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/cpm_norm.Rd -------------------------------------------------------------------------------- /man/directed_nes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/directed_nes.Rd -------------------------------------------------------------------------------- /man/ecdf_ges.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/ecdf_ges.Rd -------------------------------------------------------------------------------- /man/ecdf_norm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/ecdf_norm.Rd -------------------------------------------------------------------------------- /man/fast_pca.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/fast_pca.Rd -------------------------------------------------------------------------------- /man/figures/fig_abt-markers.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/figures/fig_abt-markers.jpg -------------------------------------------------------------------------------- /man/figures/fig_qc.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/figures/fig_qc.jpg -------------------------------------------------------------------------------- /man/figures/fig_vip-clust.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/figures/fig_vip-clust.jpg -------------------------------------------------------------------------------- /man/figures/fig_vip-markers.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/figures/fig_vip-markers.jpg -------------------------------------------------------------------------------- /man/figures/fig_vip-mrs.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/figures/fig_vip-mrs.jpg -------------------------------------------------------------------------------- /man/get_mr_set.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/get_mr_set.Rd -------------------------------------------------------------------------------- /man/group_colors.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/group_colors.Rd -------------------------------------------------------------------------------- /man/human_regulators.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/human_regulators.Rd -------------------------------------------------------------------------------- /man/internal_ges.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/internal_ges.Rd -------------------------------------------------------------------------------- /man/kappa_cluster_mrs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/kappa_cluster_mrs.Rd -------------------------------------------------------------------------------- /man/kw_cluster_mrs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/kw_cluster_mrs.Rd -------------------------------------------------------------------------------- /man/log_kw.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/log_kw.Rd -------------------------------------------------------------------------------- /man/louvain_clust.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/louvain_clust.Rd -------------------------------------------------------------------------------- /man/louvain_k.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/louvain_k.Rd -------------------------------------------------------------------------------- /man/make_mds.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/make_mds.Rd -------------------------------------------------------------------------------- /man/make_metacells.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/make_metacells.Rd -------------------------------------------------------------------------------- /man/make_umap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/make_umap.Rd -------------------------------------------------------------------------------- /man/matrix_convert_genes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/matrix_convert_genes.Rd -------------------------------------------------------------------------------- /man/matrix_narnea.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/matrix_narnea.Rd -------------------------------------------------------------------------------- /man/meta_narnea.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/meta_narnea.Rd -------------------------------------------------------------------------------- /man/mouse_regulators.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/mouse_regulators.Rd -------------------------------------------------------------------------------- /man/mt_genes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/mt_genes.Rd -------------------------------------------------------------------------------- /man/narnea_combine.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/narnea_combine.Rd -------------------------------------------------------------------------------- /man/nes_covariance.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/nes_covariance.Rd -------------------------------------------------------------------------------- /man/network_match_narnea.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/network_match_narnea.Rd -------------------------------------------------------------------------------- /man/opt_kappa.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/opt_kappa.Rd -------------------------------------------------------------------------------- /man/pairwise_cluster_mrs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/pairwise_cluster_mrs.Rd -------------------------------------------------------------------------------- /man/pam_k.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/pam_k.Rd -------------------------------------------------------------------------------- /man/pbmc.raw.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/pbmc.raw.Rd -------------------------------------------------------------------------------- /man/pf_norm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/pf_norm.Rd -------------------------------------------------------------------------------- /man/pflpf_norm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/pflpf_norm.Rd -------------------------------------------------------------------------------- /man/qc_filt.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/qc_filt.Rd -------------------------------------------------------------------------------- /man/qc_plot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/qc_plot.Rd -------------------------------------------------------------------------------- /man/quantile_breaks.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/quantile_breaks.Rd -------------------------------------------------------------------------------- /man/read10X.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/read10X.Rd -------------------------------------------------------------------------------- /man/scale_ges.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/scale_ges.Rd -------------------------------------------------------------------------------- /man/sig_features.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/sig_features.Rd -------------------------------------------------------------------------------- /man/stouffer_cluster_mrs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/stouffer_cluster_mrs.Rd -------------------------------------------------------------------------------- /man/stouffer_narnea.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/stouffer_narnea.Rd -------------------------------------------------------------------------------- /man/undirected_nes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/undirected_nes.Rd -------------------------------------------------------------------------------- /man/unweighted_integration.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/unweighted_integration.Rd -------------------------------------------------------------------------------- /man/weighted_integration.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/man/weighted_integration.Rd -------------------------------------------------------------------------------- /vignettes/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | *.R 3 | -------------------------------------------------------------------------------- /vignettes/general-workflow.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/vignettes/general-workflow.Rmd -------------------------------------------------------------------------------- /vignettes/pisces_pbmc.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/califano-lab/PISCES/HEAD/vignettes/pisces_pbmc.Rmd --------------------------------------------------------------------------------