Skip to content

Add more examples/ ; improved singlecell utils #22

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
afloresep merged 6 commits into from
Apr 2, 2026
Merged

Add more examples/ ; improved singlecell utils #22

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
81c946d
add NLP example
afloresep Mar 31, 2026
d3a779e
add singlecell helpers: subset_anndata, sample_obs_indices, obs_to_nu…
afloresep Apr 2, 2026
9b11b31
add tests for singlecell helpers
afloresep Apr 2, 2026
c26b70c
update examples: add singlecell section to README, format mnist and p…
afloresep Apr 2, 2026
4a0cc6c
add examples: cub200 birds, emnist, flowers, word embeddings, wikiart
afloresep Apr 2, 2026
5967caf
Merge branch 'master' into layout_generators
afloresep Apr 2, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions examples/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,13 @@
|---------|-------------|--------------|
| [`afdb_clusters_tmap.py`](afdb_clusters_tmap.py) | AlphaFold DB: 2.3M structural clusters from Foldseek | Precomputed `KNNGraph`, taxonomy resolution, `node_diversity`, large-scale pipeline |

## Single-cell

| Example | Description | Key features |
|---------|-------------|--------------|
| [`singlecell_trajectory_tmap.py`](singlecell_trajectory_tmap.py) | Murine lung regeneration trajectory from an official AnnData `.h5ad` | `from_anndata`, `cell_metadata`, `marker_scores`, pseudotime via `distances_from()` |
| [`singlecell_reprogramming_tmap.py`](singlecell_reprogramming_tmap.py) | Morris fibroblast-to-iEP direct reprogramming trajectory from an official AnnData `.h5ad` | Backed AnnData filtering, explicit root/target anchors, reference pseudotime comparison |

## Quick start

The fastest way to try TMAP:
Expand Down
Loading