brainfo

orca in R failed

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I used rstudio-server with rmarkdown. and I just wrote `orca(fig, "time_vocano.pdf")` in .Rmd file. the error is this: ``` Warning: 'orca' is deprecated. Use 'kaleido' instead. See help("Deprecated") Error: System...

any way from bowtie2 aligned bam file or filtered pairs file to the tadbit compatible bam file?

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Hi, What if I already have bowtie2 aligned .bam file or filtered pairs file, wanna using tadbit to call tad? How to make tadbit required bam format file from normal...

Hi I'm using sc.external.pp.mnn_correct to correct three batches with in total 13383 obs and 6214 vars in jupyterlab. I'm using: scanpy==1.7.2 anndata==0.8.0 umap==0.5.2 numpy==1.21.5 scipy==1.8.0 pandas==1.4.1 scikit-learn==1.0.2 statsmodels==0.13.2 python-igraph==0.9.9 with...

When importing mnnpy version 0.1.9.5 with python 3.8.8, it failed with error `[1] 1768057 illegal hardware instruction (core dumped) python` but python 3.8.8 can import 0.1.9.3

input data with pearson residuals workflow

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Hi, nice work! If I would to use [pearson residuals ](https://scanpy.readthedocs.io/en/stable/generated/scanpy.experimental.pp.highly_variable_genes.html)to normalize and find hvgs, I'm wondering when use other external apis such as scrublet. currently in the [doc](https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.scrublet.html): >...

Large number of dataframe columns cause hdf5 write error: Unable to create attribute (object header message is too large)

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- [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. - [ ]...

Hey, I really don't know if this could be called an issue. Since in the paper justifying [square root normalization ](https://www.biorxiv.org/content/10.1101/770388v3.full)for visualization and clustering? and the [Pearson residue](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02451-7) normalizes and...

python 3.10 support

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since collections in py 3.10 put MutableSet, MutableMapping, etc. in collections.abc insert these lines ``` import sys if sys.version_info.major == 3 and sys.version_info.minor >= 10: from collections.abc import MutableSet collections.MutableSet...

Hi, anndata has layers to save more information. I'm wondering if scanpy_cello can support the selection of layers to use. Thus we don't need to save separate object files to...

failed with test data

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**OS/Platform** - OS/Platform: Ubuntu 20.04.3 LTS - Conda version: conda 4.11.0 - Pipeline version: v1.1.8 - Caper version: v2.1.3 **Caper configuration file** ``` backend=local # Hashing strategy for call-caching (3...