Comments (1)
I think you could get better help on Stackoverflow or https://discuss.scverse.org/
If pip
reports “Requirement already satisfied” but scanpy can’t import it, then the environment you run pip
on is not the same you run scanpy in (or the environment is broken and something caused the metadata to be there while the actual package isn’t)
If you run pip --version
, it should tell you its location. That location will probably be different from /opt/miniconda3/envs/scanpyenvt/
, so you need to make sure you use the correct pip, either by doing
/opt/miniconda3/envs/scanpyenvt/bin/pip install ...
or by activating it.
As said, if you have questions, please go to one of the forums that have a lot of people who can help you!
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Related Issues (20)
- AttributeError (sc.pl.stacked_violin) HOT 1
- A neighbors error HOT 1
- sc.pp.neighbors error: api_export.__init__() got an unexpected keyword argument 'metaclass'
- Change the size of gene symbol labels on x axis
- Incorrect column label and color assign when using 'rank_genes_groups_stacked_violin' with 'swap_axes=True'
- `hvg` selects more genes than asked for HOT 5
- scanpy.pl.highest_expr_genes boxplots contain extra gene rows
- Enhance scanpy.tl.rank_gene_groups with additional filters (min_pct, etc.,)
- ingest confidence thresholding HOT 2
- score_genes doesn’t produce the expected number of bins of equal or approximately equal size
- score_genes fails completely when the gene set has zero expression in some cells HOT 2
- Don't prepend `"X_"`
- the colors saved in the .uns are not used when pl embeddings
- sc.tl.dendrogram no longer(?) works in backed mode HOT 1
- `sc.pl.dotplot` does not show the dendrogram HOT 2
- Depend on session-info2 HOT 1
- Trajectory inference tutorial: error when running a code
- Rank_genes_groups -> does not return Axes
- Umap parallel
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