anndata for R has a new home!

[This article was first published on R | Robrecht Cannoodt, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

anndata for R is brings h5ad processing to R with the same easy-to-use interface as the Python anndata API. No longer do you have to fiddle with hdf5r, reticulate or one of the many conversion functions.

The code base for anndata for R has been moved from rcannood/anndata to dynverse/anndata and with it got a fancy new homepage to be able to browse the documentation from:!

If you haven’t yet, please give anndata for R a try! We’ve found that by using anndata for R, interacting with other anndata-based Python packages becomes super easy¹! Below is a small demonstration.

Download and load dataset

Let’s use a 10x dataset from the 10x genomics website. You can download it to an anndata object with scanpy as follows:

sc <- import("scanpy")
url <- ""
ad <- sc$read_10x_h5("dataset.h5", backup_url = url)
## AnnData object with n_obs × n_vars = 5377 × 36601
## var: 'gene_ids', 'feature_types', 'genome'

Preprocessing dataset

The resuling dataset is a wrapper for the Python class but behaves very much like an R object:

ad[1:5, 3:5]
## View of AnnData object with n_obs × n_vars = 5 × 3
## var: 'gene_ids', 'feature_types', 'genome'
## [1] 5377 36601

You can still call scanpy functions on it, for example to perform preprocessing.

sc$pp$filter_cells(ad, min_genes = 200)
sc$pp$filter_genes(ad, min_cells = 3)

Analysing your dataset in R

You can seamlessly switch back to using your dataset with other R functions. For example, calculating the rowMeans of the expression matrix.

## 0.05451418 0.13627126 0.12637224 0.13958617
## 0.05979424 0.11365747 0.05011727 0.14347849
## 0.12979302 0.12366312

Additional thoughts

¹ When it works. While anndata for R has certainly been useful for us, there is still a lot left to implement. For example, using h5ad-backed AnnData objects does not work yet. If you do encounter an issue, let us know by means of a GitHub Issue. Make sure to include a reproducible example!

To leave a comment for the author, please follow the link and comment on their blog: R | Robrecht Cannoodt. offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)