scanpy
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scverse
Single-cell analysis in Python. Scales to >1M cells.
--- Hello there, I am relatively new at scanpy, and am getting the following error upon trying to plot the PCA components. Even though I am getting a plot, it...
I would like to add `bento` to the Ecosystems page, a toolkit I have developed for subcellular spatial transcriptomics analysis. Please let me know if I need to add anything...
- [ ] Additional function parameters / changed functionality / changed defaults? - [ ] New analysis tool: A simple analysis tool you have been using and are missing in...
I think it makes sense to deprecate and then remove `sc.read_visium`. and `sc.pl.spatial` since I don't plan to maintain it here anymore and updated versions are present in Squidpy. What...
Hi, all As new to scanpy, I met strange things when using `sc.read_csv`, the `obs` are genes and the `var` are cells ``` adata = sc.read_csv(x) data # AnnData object...
I'm trying to load the GSE164690 data using sc.read_10x_h5(), for which I'm including the path to the folders which contain the barcodes.tsv, features.tsv and matrix.mtx but I'm getting the IsADirectoryError...
@dkobak @ivirshup @Koncopd This is a first stab #1233. Features - [X] Construct t-SNE embeddings - [ ] Recipes - [ ] Ingest functionality As discussed, this PR currently implements...
I was wondering whether it is possible to plot this split dotplot (in this case, half of a dot represents mRNA levels while the other half about protein)?  This...
- [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on the latest version of scanpy. - [ ]...
In pl.pca_loagings(), there should be an option to limit the number of points plotted (basically n_points from ranking) Why: I recently used the AnnData/scanpy suite to perform some analysis on...
