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https://github.com/atarashansky/sctransformpy

A python port of the R package SCTransform:

https://github.com/atarashansky/sctransformpy

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (6.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A python port of the R package SCTransform:

Basic Info
  • Host: GitHub
  • Owner: atarashansky
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 96.7 KB
Statistics
  • Stars: 20
  • Watchers: 2
  • Forks: 5
  • Open Issues: 2
  • Releases: 0
Created over 5 years ago · Last pushed about 5 years ago
Metadata Files
Readme

README.md

SCTransformPy

This is a python port of the R package SCTransform.

Currently, I only use log UMI counts as a single latent variable (the default in the R package). I'm planning on allowing the user to define custom regression models as is done in the R implementation.

Implementation notes: - Poisson regression is done using the statsmodels package and parallelized with multiprocessing. - Improved Sheather & Jones bandwidth calculation is implemented by the KDEpy package. - Estimating theta using MLE was translated from the theta.ml function in R. - Pearson residuals are automatically clipped to be in the range [0, sqrt(N/30)] where N is the number of cells. This ensures that sparsity structure is preserved in the data. Practically, the results do not change much when allowing for dense, negative values.

TODO

  • Provide comparison between the python and R implementations here to show that results are highly similar.
  • Clean up code and prepare for integration with scanpy.

Owner

  • Login: atarashansky
  • Kind: user

GitHub Events

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  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 13
  • Total Committers: 2
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.154
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
atarashansky t****n@s****u 11
atarashansky a****y@c****g 2
Committer Domains (Top 20 + Academic)
czbiohub.org: 1 stanford.edu: 1

Issues and Pull Requests

Last synced: 12 months ago

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  • Total issues: 2
  • Total pull requests: 0
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  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
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  • Merged pull requests: 0
  • Bot issues: 0
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Top Authors
Issue Authors
  • Bastien-mva (1)
  • fteufel (1)
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Dependencies

setup.py pypi
  • KDEpy *
  • anndata *
  • numpy *
  • pandas *
  • scipy *
  • statsmodels *