Man pages for alexyermanos/Echidna
Single Cell Immune Repertoire and Transcriptome Simulation
| clonofreq | Plot clonal frequency barplot of the outout simulated data |
| clonofreq.isotype.data | Get information about the clonotype counts grouped by... |
| clonofreq.isotype.plot | Get information about the clonotype counts grouped by... |
| clonofreq.trans.data | Get information about the clonotype counts grouped by... |
| clonofreq.trans.plot | Get information about the clonotype counts grouped by... |
| cluster.id.igraph | Get clone network igraphs colored by seurat cluster id. |
| get.avr.mut.data | Get information about somatic hypermutation in the... |
| get.avr.mut.plot | Get information about somatic hypermutation in the... |
| get.barplot.errorbar | Return a barplot of mean and standard error bar of certain... |
| get.elbow | Get the seurat object from simulated transciptome output. |
| get.n.node.data | Get the number of unique variants in each clone in a vector.... |
| get.n.node.plot | Get the number of unique variants in each clone in a vector... |
| get.seq.distance | Computing sequence distance according to the number of... |
| get.umap | Further process the the seurat object from simulated... |
| get.vgu.matrix | Get paired v gene heavy chain and light chain matrix on... |
| no.empty.node | Get clone network igraphs without empty mode. Empty node... |
| select.top | Get the index of top ranking clones. |
| simulate_repertoire | Simulate immune repertoire and transcriptome data |
| umap.top.highlight | Set idents for top abundant clones in Seurat object, get... |
| vae_generate | Simulate B or T cell receptor sequences by variational... |
