AddDist | Generates a distance matrix for the active assay of the given... |
AddGES | Generates a GES, either internally or against an external... |
AddMDS | Generates a Multidimensional Scaling (MDS) for the active... |
AddNetworks | Adds networks to a Seurat object with a 'PISCESpact' assay. |
AddPCA | Generates a principle component analysis (PCA) for the active... |
AddPISCESAssay | Adds a named assay 'PISCES' to a Seurat object. |
AddUMAP | Generates a UMAP for the active assay of the given object. |
ARACNeTable | Saves a matrix in a format for input to ARACNe |
cluster_mr_heatmap | Generates a heatmap of cluster-specific MR activity.... |
cluster_mr_volcano | Generates cluster-specific volcano plots from the given... |
cluster_pair_mr_volcano | Generates cluster-specific volcano plots from the given... |
cluster_signature_mrs | Identifies cluster specific master regulators by generating... |
cohen_kappa | Calculates the Cohen's Kappa between two categorical vectors. |
color_levels | Returns color gradient for the specified data type... |
combine_nes | Generates a final NES from the combination of the Directed... |
convert_genes | Converts a list of gene names from 'from' to 'to'... |
cor_dist | Generates a distance matrix using the square root of (1 -... |
cpm_norm | Peforms a CPM normalization on the given matrix. |
directed_nes | Computes the Directed NES |
ecdf_ges | Generates a gene expression signature through an ECDF, either... |
ecdf_norm | Normalizes values in the test vector based on the ECDF of the... |
fast_pca | Generates the specified number of PCs using RSpectra. |
get_mr_set | Returns set of candidate master regulators or markers from... |
group_colors | Identifies a vector of colors for a given number of groups. |
human_regulators | Human Regulator sets as Gene Names |
internal_ges | Generates a single-sample, internal GES. |
kappa_cluster_mrs | Identifies cluster master regulators based on Cohen's Kappa. |
KNN | Generates a KNN matrix. |
kw_cluster_mrs | Identifies cluster-specific master regulators using a... |
log_kw | Returns a log p-value from a Kruskal-Wallis test for the... |
louvain_clust | Runs Louvain clusering on the given object with the specified... |
LouvainClust | Performs louvain clustering on the active assay of the given... |
louvain_k | Optimizes Louvain clustering over a range of number of... |
make_mds | Generates an MDS using base R functionality. |
make_metacells | Generates meta cells for each cluster |
make_umap | Generates a UMAP using the uwot package. |
matrix_convert_genes | Converts the gene rownames of a matrix from the 'from' to... |
matrix_narnea | Runs the NaRnEA algorithm on multiple samples / regulons... |
meta_narnea | Runs MetaNaRnEA using the given ges matrix and network list. |
MinAssignments | Calculates the Phi matrix that minimizes the objective for... |
MinClusters | Calculates the optimal centers given data and cluster... |
mouse_regulators | Mouse Regulator sets as Gene Names |
mt_genes | Mosue / human mitochondrial genes in either GN or ENSG... |
MWKMeans | Generates a multiway k-means given the data and starting... |
MWUMrs | Identifies cluster specific master regulators using the... |
narnea_combine | Generates two 3D matrices (PES/NES) from a list of NaRnEA... |
nes_covariance | Compute the Covariance of the Directed and Undirected NES. |
network_match_narnea | Performs NaRnEA on multiple samples using network matching.... |
NormalizeExpression | Normalizes gene expression in the PISCESgexp assay. Stores... |
ObjectiveValue | Calculates the value of the objective function for optimizing... |
opt_kappa | Determines the optimal possible Cohen's Kappa that can be... |
pairwise_cluster_mrs | Identified MRs based on a pairwise comparison of clusters. |
PAMClust | Performs PAM clustering on the active assay of the given... |
pam_k | Optimizes PAM clustering over a range of cluter numbers 'k'... |
pbmc.raw | Single-Cell RNASeq from PBMC data |
pflpf_norm | Performs PF log1 PF norm normalization. |
pf_norm | Normalizes a matrix using one round of proportional fitting. |
PISCESActivity | Generates protein activity readout using the NaRnEA... |
PISCESViper | Runs VIPER on a seurat.obj that has the appropriately... |
qc_filt | Filters raw gene expression data based on depth, unique... |
qc_plot | Generates QC violin plots for depth, detected genes, and MT... |
quantile_breaks | Generates breaks for a color scale based on quantiles. |
read10X | Read in data in 10x format |
RegProcess | Processes ARACNe results into a regulon object compatible... |
scale_ges | Generates a gene expression signature by scaling and... |
sig_features | Returns a list of significant proteins for each sample... |
stouffer_cluster_mrs | Returns an MR object with MRs selected via Stouffer... |
stouffer_narnea | Returns cluster-integrated NaRnEA results using Stouffer's... |
TwoMatVipSim | Returns the viperSimilarity of the elements of two matrices. |
undirected_nes | Computes the Undirected NES |
unweighted_integration | Integrates 3D arrays of NaRnEA results generated by... |
ViperMerge | Merges two viper matrices, giving priority to one over the... |
weighted_integration | Integrates 3D arrays of NaRnEA results generated by... |
WeightedVIPER | MetaVIPER implementation that will perform a weighted... |
WriteMetaCells | Generates metacells from the given Seurat object. Rquires... |
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