scanpy-tutorials

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Further improvements for the advanced visualisation tutorial

3

- [ ] More notes on how to deal with more complex plots, e.g. DotPlot - [ ] Split up dotplot https://github.com/scverse/scanpy/issues/1956 - [ ] Legend hierarchy https://github.com/scverse/scanpy/issues/2024 - [...

Hrovatin

Automate tutorial building in CI

3

See https://github.com/scverse/scverse-tutorials/blob/main/.github/workflows/execute-nbs.yaml This fixes: - #28 - #36 - #45 - #66 - #74

flying-sheep

Hi there, I downloaded and ran the trajectory inference [Jupyter notebook](https://github.com/scverse/scanpy-tutorials/blob/master/paga-paul15.ipynb). I could run smoothly, but I cannot get the plot where cells are overlayed to the trajectory. (As you...

OXPHOS

In the tutorial "Integrating spatial data with scRNA-seq using scanorama", I could not download the pre-processed h5ad file, which is embedded(linked) to the following sentence: "Conveniently, you can also download...

id-f

File not found error

3

Hi I am new to Scanpy and I continue to encounter this "FileNotFoundError: Did not find file data/filtered_gene_bc_matrices/hg19/matrix.mtx.gz. I have unzipped the file but that is of no use. Would...

tht17

I am getting an error with sc.pl.paga_path. It doesnt plot genes that my data has - i doubled checked my gene, it is in adata.var_names... if i use a gene...

xlw1207

Hi, I am getting this error while adding a new column for MT genes. What is that I am doing wrong? ```py adata = sc.read_10x_h5(dir_path + 'filtered_feature_bc_matrix.h5') adata.var_names_make_unique() print(adata.X) print(adata.obs['sample'].value_counts())...

preetida

updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.5 → v0.6.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.5...v0.6.7)

pre-commit-ci[bot]

pseudobulking + DE tutorial

3

See https://decoupler.readthedocs.io/en/latest/notebooks/scell/rna_psbk.html for a starting point, but some questions/TODOs remain: 1. decoupler has some nice plotting functionality for `filter_samples`, `filter_by_prop` etc - do we want to keep that? Migrate to...

ilan-gold

They lead to issues like https://github.com/scverse/scanpy/issues/3584

flying-sheep