Man pages for califano-lab/PISCES
Protein Activity Inferecne in Single Cells

AddDistGenerates a distance matrix for the active assay of the given...
AddGESGenerates a GES, either internally or against an external...
AddMDSGenerates a Multidimensional Scaling (MDS) for the active...
AddNetworksAdds networks to a Seurat object with a 'PISCESpact' assay.
AddPCAGenerates a principle component analysis (PCA) for the active...
AddPISCESAssayAdds a named assay 'PISCES' to a Seurat object.
AddUMAPGenerates a UMAP for the active assay of the given object.
ARACNeTableSaves a matrix in a format for input to ARACNe
cluster_mr_heatmapGenerates a heatmap of cluster-specific MR activity....
cluster_mr_volcanoGenerates cluster-specific volcano plots from the given...
cluster_pair_mr_volcanoGenerates cluster-specific volcano plots from the given...
cluster_signature_mrsIdentifies cluster specific master regulators by generating...
cohen_kappaCalculates the Cohen's Kappa between two categorical vectors.
color_levelsReturns color gradient for the specified data type...
combine_nesGenerates a final NES from the combination of the Directed...
convert_genesConverts a list of gene names from 'from' to 'to'...
cor_distGenerates a distance matrix using the square root of (1 -...
cpm_normPeforms a CPM normalization on the given matrix.
directed_nesComputes the Directed NES
ecdf_gesGenerates a gene expression signature through an ECDF, either...
ecdf_normNormalizes values in the test vector based on the ECDF of the...
fast_pcaGenerates the specified number of PCs using RSpectra.
get_mr_setReturns set of candidate master regulators or markers from...
group_colorsIdentifies a vector of colors for a given number of groups.
human_regulatorsHuman Regulator sets as Gene Names
internal_gesGenerates a single-sample, internal GES.
kappa_cluster_mrsIdentifies cluster master regulators based on Cohen's Kappa.
KNNGenerates a KNN matrix.
kw_cluster_mrsIdentifies cluster-specific master regulators using a...
log_kwReturns a log p-value from a Kruskal-Wallis test for the...
louvain_clustRuns Louvain clusering on the given object with the specified...
LouvainClustPerforms louvain clustering on the active assay of the given...
louvain_kOptimizes Louvain clustering over a range of number of...
make_mdsGenerates an MDS using base R functionality.
make_metacellsGenerates meta cells for each cluster
make_umapGenerates a UMAP using the uwot package.
matrix_convert_genesConverts the gene rownames of a matrix from the 'from' to...
matrix_narneaRuns the NaRnEA algorithm on multiple samples / regulons...
meta_narneaRuns MetaNaRnEA using the given ges matrix and network list.
MinAssignmentsCalculates the Phi matrix that minimizes the objective for...
MinClustersCalculates the optimal centers given data and cluster...
mouse_regulatorsMouse Regulator sets as Gene Names
mt_genesMosue / human mitochondrial genes in either GN or ENSG...
MWKMeansGenerates a multiway k-means given the data and starting...
MWUMrsIdentifies cluster specific master regulators using the...
narnea_combineGenerates two 3D matrices (PES/NES) from a list of NaRnEA...
nes_covarianceCompute the Covariance of the Directed and Undirected NES.
network_match_narneaPerforms NaRnEA on multiple samples using network matching....
NormalizeExpressionNormalizes gene expression in the PISCESgexp assay. Stores...
ObjectiveValueCalculates the value of the objective function for optimizing...
opt_kappaDetermines the optimal possible Cohen's Kappa that can be...
pairwise_cluster_mrsIdentified MRs based on a pairwise comparison of clusters.
PAMClustPerforms PAM clustering on the active assay of the given...
pam_kOptimizes PAM clustering over a range of cluter numbers 'k'...
pbmc.rawSingle-Cell RNASeq from PBMC data
pflpf_normPerforms PF log1 PF norm normalization.
pf_normNormalizes a matrix using one round of proportional fitting.
PISCESActivityGenerates protein activity readout using the NaRnEA...
PISCESViperRuns VIPER on a seurat.obj that has the appropriately...
qc_filtFilters raw gene expression data based on depth, unique...
qc_plotGenerates QC violin plots for depth, detected genes, and MT...
quantile_breaksGenerates breaks for a color scale based on quantiles.
read10XRead in data in 10x format
RegProcessProcesses ARACNe results into a regulon object compatible...
scale_gesGenerates a gene expression signature by scaling and...
sig_featuresReturns a list of significant proteins for each sample...
stouffer_cluster_mrsReturns an MR object with MRs selected via Stouffer...
stouffer_narneaReturns cluster-integrated NaRnEA results using Stouffer's...
TwoMatVipSimReturns the viperSimilarity of the elements of two matrices.
undirected_nesComputes the Undirected NES
unweighted_integrationIntegrates 3D arrays of NaRnEA results generated by...
ViperMergeMerges two viper matrices, giving priority to one over the...
weighted_integrationIntegrates 3D arrays of NaRnEA results generated by...
WeightedVIPERMetaVIPER implementation that will perform a weighted...
WriteMetaCellsGenerates metacells from the given Seurat object. Rquires...
califano-lab/PISCES documentation built on Jan. 11, 2023, 5:34 a.m.