Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/alleninstitute/enhancerbenchmark

https://github.com/alleninstitute/enhancerbenchmark

Science Score: 57.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ✓
    Institutional organization owner
    Organization alleninstitute has institutional domain (alleninstitute.org)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.6%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • Language: Python
  • Default Branch: main
  • Size: 7.04 MB
Statistics
  • Stars: 2
  • Watchers: 4
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created over 1 year ago · Last pushed 10 months ago
Metadata Files
Readme

README.markdown

WashU

Summary

Single-cell sequencing technologies enable molecular profiling of millions of cells to define atlases, or catalogs, of cell types across tissues and species. Recent advancements enable measurement of multiple genomic features (e.g. RNA and open chromatin) from the same cell. Multi-omic profiling of the brain across species enables high-resolution alignment of ‘homologous’ cell types that have conserved and specialized molecular features (Hodge et al. 2019, Jorstad et al. 2022, Zemke et al. 2023).

In the BICCN competition, teams predicted cell type-specific enhancers using new multi-omics and multi-species atlases of cell types in the primary motor cortex. Teams were evaluated against in vivo activity of enhancers in the mouse brain from a collection of several hundred enhancers that were experimentally screened Ben-Simon et al. 2024; addgene. Progress will serve as a foundation for targeted exploration of cell types in brain circuitry across species.

Evaluate your method

We designed the benchmark metric for the challenge to be used to evaluate new approaches in the context of the current state-of-the-art enhancer prioritization methods. Following the guidelines in our submissions and data pages please self-evaluate using the benchmark metric, and enhancer validation tables provided in assets of this github. We encourage method developers to then create a pull request to our leaderboard page with your results and submission files.

Pages

  • About : General information about the BICCN Challenge and benchmark metric.
  • Data : Data overview and summary of files.
  • Submissions : Detaials for the expected submission format.
  • Evaluation : Benchmark metric summary.

Leaderboard

  • Leaderboard : Challenge and running leaderboard for new method submissions.

Ask a question

We will be using the Github issues page for this website, found here, as a means for discussion and questions regarding the challenge.

Organizing committee

| | | | | --- | --- | --- | --- | Nelson Johansen | Bosiljka Tasic | Trygve Bakken | Ed Lein | | Bing Ren | | | | Joe Ecker | | |

Funding support

  • Allen Institute for Brain Science
  • U19MH11483 to J.R.E and E.M.C
  • U19MH114831-04s1 to J.R.E. and B.R.
  • 5U01MH121282 to J.R.E and M.M.B
  • UM1HG011585 to B.R.

Links to methods

https://github.com/AllenInstitute/PeakRankR

https://github.com/ytanaka-bio/cisMultiDeep

https://labshare.cshl.edu/shares/gillislab/resource/HiC

CREsted: Cis Regulatory Element Sequence Training, Explanation, and Design.

Citation

Johansen, N. J., Kempynck, N., (2024). Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex. bioRxiv, 2024-08. https://doi.org/10.1101/2024.08.21.609075

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total
  • Issues event: 1
  • Issue comment event: 1
  • Member event: 1
  • Push event: 4
Last Year
  • Issues event: 1
  • Issue comment event: 1
  • Member event: 1
  • Push event: 4

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 21
  • Total Committers: 2
  • Avg Commits per committer: 10.5
  • Development Distribution Score (DDS): 0.048
Past Year
  • Commits: 21
  • Committers: 2
  • Avg Commits per committer: 10.5
  • Development Distribution Score (DDS): 0.048
Top Committers
Name Email Commits
Nelson Johansen n****n@a****g 20
marcusjhooper 3****r 1
Committer Domains (Top 20 + Academic)
alleninstitute.org: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 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
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • XuYuanchi (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

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