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simplex_chrombpnet

Implementing simplex encoding to chrombpnet

https://github.com/bhummanat/simplex_chrombpnet

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Scientific vocabulary similarity
    Low similarity (1.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Implementing simplex encoding to chrombpnet

Basic Info
  • Host: GitHub
  • Owner: Bhummanat
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 31.7 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created 11 months ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Citation

README.md

This repo contains modified version of https://github.com/kundajelab/chrombpnet.

Simplex Encoding

Main changes this repo aim to introduce is simplex encoding as implemented in https://github.com/zang-lab/SELMA.

Change log

Owner

  • Name: Bhummanat Sittipongpittaya
  • Login: Bhummanat
  • Kind: user
  • Company: University of Virginia

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Pampari"
  given-names: "Anusri"
  orcid: "https://orcid.org/0000-0002-6579-4070"
- family-names: "Shcherbina"
  given-names: "Anna"
- family-names: "Nair"
  given-names: "Surag"
- family-names: "Schreiber"
  given-names: "Jacob"
- family-names: "Patel"
  given-names: "Aman"
- family-names: "Wang"
  given-names: "Austin"
- family-names: "Kundu"
  given-names: "Soumya"
- family-names: "Shrikumar"
  given-names: "Avanti"
- family-names: "Kundaje"
  given-names: "Anshul"
title: "Bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants."
version: 0.1.1
doi: 10.5281/zenodo.7567627
date-released: 2023-01-24
url: "https://github.com/kundajelab/chrombpnet"

GitHub Events

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  • Push event: 8
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Last Year
  • Push event: 8
  • Create event: 1

Dependencies

setup.py pypi
.github/workflows/latest-docker-image.yml actions
  • actions/checkout v2 composite
requirements.txt pypi
  • deepdish ==0.3.7
  • deeplift ==0.6.13.0
  • h5py >=2.10.0
  • kundajelab-shap ==1
  • matplotlib >=3.3.1
  • matplotlib-venn ==0.11.6
  • modisco ==0.5.16.0
  • modisco-lite ==2.0.7
  • numpy ==1.23.4
  • pandas >=1.3.4
  • protobuf ==3.20
  • pyfaidx ==0.6.1
  • scikit-learn >=1.1.2
  • scipy >=1.4.1
  • tensorflow ==2.8.0
  • tensorflow-estimator ==2.8.0
  • tensorflow-probability ==0.15.0
  • tqdm ==4.48.2
  • weasyprint ==52.5
chrombpnet.egg-info/requires.txt pypi
  • deepdish ==0.3.7
  • deeplift ==0.6.13.0
  • h5py >=2.10.0
  • kundajelab-shap ==1
  • matplotlib >=3.3.1
  • matplotlib-venn ==0.11.6
  • modisco ==0.5.16.0
  • modisco-lite ==2.0.7
  • numpy ==1.23.4
  • pandas >=1.3.4
  • protobuf ==3.20
  • pyfaidx ==0.6.1
  • scikit-learn >=1.1.2
  • scipy >=1.4.1
  • tensorflow ==2.8.0
  • tensorflow-estimator ==2.8.0
  • tensorflow-probability ==0.15.0
  • tqdm ==4.48.2
  • weasyprint ==52.5