Filter, plot and explore single-cell RNA-seq data with Scanpy (Python)
Aug 25, 2023 · Training material and practicals for all kinds of single cell analysis (particularly scRNA-seq!).
Clustering 3K PBMCs with Scanpy - Galaxy Training Network
Dec 19, 2019 · Training material and practicals for all kinds of single cell analysis (particularly scRNA-seq!).
Inferring single cell trajectories with Scanpy
Dec 8, 2023 · Training material and practicals for all kinds of single cell analysis (particularly scRNA-seq!).
Inferring single cell trajectories with Scanpy (Python)
Apr 7, 2021 · Training material and practicals for all kinds of single cell analysis (particularly scRNA-seq!).
How do I create AnnData object from a pandas data frame count matrix?
Dec 3, 2020 · I am trying to use the Scanpy Python package to analyze some single-cell data. I read a count matrix (a .tsv file) in as a Pandas data frame, which has genes as the columns and rows as the …
subsetting anndata on basis of louvain clusters - Stack Overflow
Sep 16, 2020 · I want to subset anndata on basis of clusters, but i am not able to understand how to do it. I am running scVelo pipeline, and in that i ran tl.louvain function to cluster cells on basis of louvain...
Analysis of plant scRNA-Seq Data with Scanpy
Apr 8, 2021 · Training material and practicals for all kinds of single cell analysis (particularly scRNA-seq!).
ModuleNotFoundError: No module named 'scanpy' (python)
Dec 9, 2021 · I've installed scanpy, and when I check with pip show it's there: C:\Users\plain>pip show scanpy Name: scanpy Version: 1.8.2 Summary: Single-Cell Analysis in Python.
python - ImportError when importing scanpy on a Jupyter notebook …
Oct 31, 2023 · I had the same issue; I originally used following in Jupyter: !pip install scanpy After receiving the error, uninstalled scanpy, using: !python -m pip uninstall scanpy --yes And restarted the …
Newest 'scanpy' Questions - Stack Overflow
Jun 19, 2025 · I'm using scanpy/python to analyze some single-cell RNA-seq data. I want to use sc.pl.umap(show= False) in order to make ax objects, edit them, and combine them accordingly.