Man pages for rezakj/scSeqR
scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.
| add.adt | Add CITE-seq antibody-derived tags (ADT) |
| add.vdj | Add CITE-seq antibody-derived tags (ADT) |
| adt.rna.merge | Merge RNA and ADT data |
| cell.filter | Filter cells |
| cell.gating | Run PCA on the main data |
| change.clust | Change the cluster number or re-name them |
| 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.rm | Remove the cells that are in a cluster |
| clust.stats.plot | Plot nGenes, UMIs and perecent mito |
| data.aggregation | Merge multiple data frames and add the condition names to... |
| data.scale | Scale data |
| diff.exp | Differential expression (DE) analysis |
| down.sample | Down sample conditions |
| find.dim.genes | Run PCA on the main data |
| findMarkers | Find marker genes for each cluster |
| gate.to.clust | Run PCA on the main data |
| gene.plot | Make scatter, box and bar plots for genes |
| gene.stats | Make statistical information for each gene across all the... |
| heatmap.gg.plot | Create heatmaps for genes in clusters or conditions. |
| heatmap.plot | Create heatmaps for genes in clusters or conditions. |
| imm.gen | Create heatmaps or dot plots for genes in clusters to find... |
| load10x | Load 10X data as data.frame |
| lvbsc | Low Variance Batch Spacing Correction (LVBSC) |
| make.gene.model | Make a gene model for clustering |
| make.obj | Create an object of class scSeqR. |
| make.scseqr.obj | Create an object of class scSeqR. |
| man.assign.clust | Hierarchical clustering based on tSNE |
| norm.adt | Normalize ADT data. This function takes data frame and... |
| norm.data | Normalize data |
| opt.clust.num | Find optimal number of clusters. |
| opt.pcs.plot | Find optimal number of PCs for clustering |
| prep.vdj | Add CITE-seq antibody-derived tags (ADT) |
| pseudotime.tree | Pseudotime Tree |
| qc.stats | Calculate the number of UMIs and genes per cell and... |
| run.clustering | Clustering the data |
| run.diff.st | Differentiation spacetime |
| run.diffusion.map | Run PHATE on PCA data (PHATE - Potential of Heat-Diffusion... |
| run.magic | Run UMAP on PCA data |
| run.pca | Run PCA on the main data |
| run.pc.tsne | Run tSNE on PCA data |
| run.tsne | Run tSNE on the main data |
| run.umap | Run UMAP on PCA data (Computes a manifold approximation and... |
| stats.plot | Plot nGenes, UMIs and perecent mito |
| top.markers | Choose top marker genes |
| tsne.plot | Plot nGenes, UMIs and perecent mito |
| volcano.ma.plot | Create MA and Volcano plots. |
