add.10x.image | Add image data to iCellR object |
add.adt | Add CITE-seq antibody-derived tags (ADT) |
add.vdj | Add V(D)J recombination data |
adt.rna.merge | Merge RNA and ADT data |
capture.image.10x | Read 10X image data |
cc | Calculate Cell cycle phase prediction |
cell.cycle | Cell cycle phase prediction |
cell.filter | Filter cells |
cell.gating | Cell gating |
cell.type.pred | Create heatmaps or dot plots for genes in clusters to find... |
change.clust | Change the cluster number or re-name them |
clono.plot | Make 2D and 3D scatter plots for clonotypes. |
clust.avg.exp | Create a data frame of mean expression of genes per cluster |
clust.cond.info | Calculate cluster and conditions frequencies |
cluster.plot | Plot nGenes, UMIs and perecent mito |
clust.ord | Sort and relabel the clusters randomly or based on pseudotime |
clust.rm | Remove the cells that are in a cluster |
clust.stats.plot | Plotting tSNE, PCA, UMAP, Diffmap and other dim reductions |
data.aggregation | Merge multiple data frames and add the condition names to... |
data.scale | Scale data |
down.sample | Down sample conditions |
find.dim.genes | Find model genes from PCA data |
findMarkers | Find marker genes for each cluster |
find_neighbors | K Nearest Neighbour Search |
g2m.phase | A dataset of G2 and M phase genes |
gate.to.clust | Assign cluster number to cell ids |
gene.plot | Make scatter, box and bar plots for genes |
gene.stats | Make statistical information for each gene across all the... |
gg.cor | Gene-gene correlation. This function helps to visulaize and... |
heatmap.gg.plot | Create heatmaps for genes in clusters or conditions. |
hto.anno | Demultiplexing HTOs |
iba | iCellR Batch Alignment (IBA) |
iclust | iCellR Clustering |
i.score | Cell cycle phase prediction |
load10x | Load 10X data as data.frame |
load.h5 | Load h5 data as data.frame |
make.bed | Make BED Files |
make.gene.model | Make a gene model for clustering |
make.obj | Create an object of class iCellR. |
myImp | Impute data |
norm.adt | Normalize ADT data. This function takes data frame and... |
norm.data | Normalize data |
opt.pcs.plot | Find optimal number of PCs for clustering |
prep.vdj | Prepare VDJ data |
pseudotime | Pseudotime |
pseudotime.knetl | iCellR KNN Network |
pseudotime.tree | Pseudotime Tree |
qc.stats | Calculate the number of UMIs and genes per cell and... |
Rphenograph | RphenoGraph clustering |
run.anchor | Run anchor alignment on the main data. |
run.cca | Run CCA on the main data |
run.clustering | Clustering the data |
run.diff.exp | Differential expression (DE) analysis |
run.diffusion.map | Run diffusion map on PCA data (PHATE - Potential of... |
run.impute | Impute the main data |
run.knetl | iCellR KNN Network |
run.mnn | Run MNN alignment on the main data. |
run.pca | Run PCA on the main data |
run.pc.tsne | Run tSNE on PCA Data. Barnes-Hut implementation of... |
run.phenograph | Clustering the data |
run.tsne | Run tSNE on the Main Data. Barnes-Hut implementation of... |
run.umap | Run UMAP on PCA Data (Computes a manifold approximation and... |
spatial.plot | Plot nGenes, UMIs and perecent mito, genes, clusters and more... |
s.phase | A dataset of S phase genes |
stats.plot | Plot nGenes, UMIs and percent mito |
top.markers | Choose top marker genes |
vdj.stats | VDJ stats |
volcano.ma.plot | Create MA and Volcano plots. |
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