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.adtAdd CITE-seq antibody-derived tags (ADT)
add.vdjAdd CITE-seq antibody-derived tags (ADT)
adt.rna.mergeMerge RNA and ADT data
cell.filterFilter cells
cell.gatingRun PCA on the main data
change.clustChange the cluster number or re-name them
clust.avg.expCreate a data frame of mean expression of genes per cluster
clust.cond.infoCalculate cluster and conditions frequencies
cluster.plotPlot nGenes, UMIs and perecent mito
clust.rmRemove the cells that are in a cluster
clust.stats.plotPlot nGenes, UMIs and perecent mito
data.aggregationMerge multiple data frames and add the condition names to...
data.scaleScale data
diff.expDifferential expression (DE) analysis
down.sampleDown sample conditions
find.dim.genesRun PCA on the main data
findMarkersFind marker genes for each cluster
gate.to.clustRun PCA on the main data
gene.plotMake scatter, box and bar plots for genes
gene.statsMake statistical information for each gene across all the...
heatmap.gg.plotCreate heatmaps for genes in clusters or conditions.
heatmap.plotCreate heatmaps for genes in clusters or conditions.
imm.genCreate heatmaps or dot plots for genes in clusters to find...
load10xLoad 10X data as data.frame
lvbscLow Variance Batch Spacing Correction (LVBSC)
make.gene.modelMake a gene model for clustering
make.objCreate an object of class scSeqR.
make.scseqr.objCreate an object of class scSeqR.
man.assign.clustHierarchical clustering based on tSNE
norm.adtNormalize ADT data. This function takes data frame and...
norm.dataNormalize data
opt.clust.numFind optimal number of clusters.
opt.pcs.plotFind optimal number of PCs for clustering
prep.vdjAdd CITE-seq antibody-derived tags (ADT)
pseudotime.treePseudotime Tree
qc.statsCalculate the number of UMIs and genes per cell and...
run.clusteringClustering the data
run.diff.stDifferentiation spacetime
run.diffusion.mapRun PHATE on PCA data (PHATE - Potential of Heat-Diffusion...
run.magicRun UMAP on PCA data
run.pcaRun PCA on the main data
run.pc.tsneRun tSNE on PCA data
run.tsneRun tSNE on the main data
run.umapRun UMAP on PCA data (Computes a manifold approximation and...
stats.plotPlot nGenes, UMIs and perecent mito
top.markersChoose top marker genes
tsne.plotPlot nGenes, UMIs and perecent mito
volcano.ma.plotCreate MA and Volcano plots.
rezakj/scSeqR documentation built on June 21, 2019, 3:34 a.m.