RNA velocity estimation in R

Documentation for package ‘velocyto.R’ version 0.6

velocyto.R-package	A short title line describing what the package does
ac	adjust colors, while keeping the vector names
armaCor	A slightly faster way of calculating column correlation matrix
filter.genes.by.cluster.expression	Filter genes by requirining minimum average expression within at least one of the provided cell clusters
find.ip.sites	identify positions of likely internal priming sites by looking for polyA/polyT stretches within annotated intronic regions
gene.relative.velocity.estimates	Estimate RNA velocity using gene-relative slopes
global.velcoity.estimates	Structure-based gene velocity estimation
pca.velocity.plot	PCA-based visualization of the velocities
read.gene.mapping.info	read in detailed molecular mapping info from hdf5 file as written out by "-d" option of velocyto.py
read.loom.matrices	Read in loom matrices of spliced/unpsliced reads as prepared by velocyto.py CLI
read.smartseq2.bams	read.smartseq2.bams
read.strtc1.bams	Read in cell-specific bam files for STRT/C1
show.velocity.on.embedding.cor	Visualize RNA velocities on an existing embedding using correlation-based transition probability matrix within the kNN graph
show.velocity.on.embedding.eu	Visualize RNA velocities on an existing embedding using Euclidean-based transition probability matrix within the kNN graph.
tSNE.velocity.plot	Joint t-SNE visualization of the velocities by joint t-SNE embedding of both current and extraploated cell positions
velocyto.R	A short title line describing what the package does