# scvelo | RNA Velocity generalized through dynamical modeling | Genomics library

## kandi X-RAY | scvelo Summary

## kandi X-RAY | scvelo Summary

RNA Velocity generalized through dynamical modeling

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### Top functions reviewed by kandi - BETA

- Convert to a velocytoLoom
- Filter genes
- Filter and normalize data
- Sum op
- Plot the state likelihoods
- Calculate the read and s
- Calculate the variance of the distribution
- Returns the distributions of the splicing potential
- Compute cell origin fates
- Get cell transition matrix
- R Compute velocity genotypes
- Compute cell fates
- Rank genes by clustering
- Plot the profiles on the grid
- Set figure parameters
- Calculate the velocity confidence interval
- Clean up layers
- Merge categorical groups
- Fit regression recovery
- Compute the least squares of x and y
- Merge two datasets
- Returns a pandas dataframe
- Displays the proportions of each layer
- Generate a simulation of splicing dynamics
- R Compute the differential kinetic test
- Plot a heatmap

## scvelo Key Features

## scvelo Examples and Code Snippets

## Community Discussions

Trending Discussions on scvelo

QUESTION

I want to subset anndata on basis of clusters, but i am not able to understand how to do it.

I am running scVelo pipeline, and in that i ran `tl.louvain`

function to cluster cells on basis of louvain. I got around 32 clusters, of which cluster 2 and 4 is of my interest, and i have to run the pipeline further on these clusters only. (Initially i had the loom file which i read in scVelo, so i have now the anndata.)

I tried using `adata.obs["louvain"]`

which gave me the cluster information, but i need to write a new anndata with only 2 clusters and process further.

Please help on how to subset anndata. Any help is highly appreciated. (Being very new to it, i am finding it difficult to get)

...ANSWER

Answered 2020-Oct-13 at 08:37If your adata.obs has a "louvain" column that I'd expect after running `tl.louvain`

, you could do the subsetting as
`adata[adata.obs["louvain"] == "2"]`

if you want to obtain one cluster and
`adata[adata.obs['louvain'].isin(['2', '4'])]`

for obtaining cluster 2 & 4.

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

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## Install scvelo

You can use scvelo like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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