annsel

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Annsel is a user-friendly library that brings familiar dataframe-style operations to AnnData objects.

It's built on the [narwhals][link-narwhals] compatibility layer for dataframes.

Take a look at the GitHub Projects board for features and future plans: [Annsel Features][link-gh-project]

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Getting started

Please refer to the [documentation][link-docs], in particular, the [API documentation][link-api].

There's also a brief tutorial on how to use all the features of annsel: [All of Annsel][link-tutorial].

Installation

You need to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing [uv][link-uv]. There are several ways to install annsel:

1. Install the most recent release:

   With uv:

   uv add annsel
   

   With pip:

   pip install annsel
   

2. Install the latest development version:

   With uv:

   uv add git+https://github.com/srivarra/annsel
   

   With pip:

   pip install git+https://github.com/srivarra/annsel.git@main
   

Examples

annsel comes with a small dataset from Cell X Gene to help you get familiar with the API.

import annsel as an

adata = an.datasets.leukemic_bone_marrow_dataset()

The dataset looks like this:

AnnData object with n_obs × n_vars = 31586 × 458
    obs: 'Cluster_ID', 'donor_id', 'Sample_Tag', 'Cell_label', 'is_primary_data', 'organism_ontology_term_id', 'self_reported_ethnicity_ontology_term_id', 'assay_ontology_term_id', 'tissue_ontology_term_id', 'Genotype', 'development_stage_ontology_term_id', 'sex_ontology_term_id', 'disease_ontology_term_id', 'cell_type_ontology_term_id', 'suspension_type', 'tissue_type', 'cell_type', 'assay', 'disease', 'organism', 'sex', 'tissue', 'self_reported_ethnicity', 'development_stage', 'observation_joinid'
    var: 'vst.mean', 'vst.variance', 'vst.vari