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snaptron-query

Web application for junction or gene expression count extraction and analysis

https://github.com/ssec-jhu/snaptron-query

Science Score: 75.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org, zenodo.org
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization ssec-jhu has institutional domain (ai.jhu.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Web application for junction or gene expression count extraction and analysis

Basic Info
Statistics
  • Stars: 1
  • Watchers: 5
  • Forks: 0
  • Open Issues: 6
  • Releases: 6
Created about 2 years ago · Last pushed 10 months ago
Metadata Files
Readme License Code of conduct Citation Codeowners Zenodo

README.md

SSEC-JHU SnapMine

CI codecov Security DOI

SSEC-JHU Logo

About

Web application for junction or gene expression count extraction and analysis: * Preprint at: Large-scale RNA-seq mining reveals ciclopirox triggers TDP-43 cryptic exons * SnapMine is deployed at: https://snapmine.idies.jhu.edu/

junction_query

Initial Setup:

  • Get the code: git clone https://github.com/ssec-jhu/snaptron-query.git
  • Then you will need to download the metadata files for the dataset of interest (or all) in a folder, renaming each file with the dataset name as prefix:

Build & Run:

Follow above setup instructions if you have not done so already. #### with Tox [running locally]: * pip install tox if you don't have it already * Make sure you are in the repo directory: cd snaptron-query * You should see the tox file: tox.ini * Run: tox -e test exec -- python -m snaptron_query.app.main_dash_app * This will have Dash running locally on http://127.0.0.1:8050/ * Ctrl+c to quit

#### with Python ecosystem [running locally]: * Make sure you are in the repo directory: cd snaptron-query * Run python3 -m snaptron_query.app.main_dash_app * This will have Dash running locally on http://127.0.0.1:8050/ * Ctrl+c to quit

Using tox to run tests

  • Run tox tox. This will run all of linting, security, test, docs and package building within tox virtual environments.
  • To run an individual step, use tox -e {step} for example:
    • tox -e format
    • tox -e test
    • tox -e build-docs
    • tox -e format

Typically, the CI tests run in github actions will use tox to run as above. See also ci.yml.

Owner

  • Name: Scientific Software Engineering Center at JHU
  • Login: ssec-jhu
  • Kind: organization
  • Email: ssec@jhu.edu
  • Location: United States of America

Accelerating Software Development for Science Research

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software in your work, please cite it using the following metadata."
authors:
- family-names: "Abbasinejad"
  given-names: "Fatemeh"
  affiliation: "Johns Hopkins University Scientific Software Engineering Center"
  orcid: "https://orcid.org/0009-0006-3239-7112"
- family-names: "Carliles"
  given-names: "Samuel"
  affiliation: "Johns Hopkins University Scientific Software Engineering Center"
  orcid: "https://orcid.org/0000-0003-0273-9776"
- family-names: "Chen"
  given-names: "Xiang"
  affiliation: "Johns Hopkins University Scientific Software Engineering Center"
  orcid: "https://orcid.org/0009-0003-6402-9822"
- family-names: "Hausen"
  given-names: "Ryan"
  affiliation: "Johns Hopkins University Scientific Software Engineering Center"
  orcid: "https://orcid.org/0000-0002-8543-761X"
- family-names: "Hunter"
  given-names: "Edward"
  affiliation: "Johns Hopkins University Scientific Software Engineering Center"
  orcid: "https://orcid.org/0000-0002-6876-001X"
- family-names: "Kluzner"
  given-names: "Vladimir"
  affiliation: "Johns Hopkins University Scientific Software Engineering Center"
  orcid: "https://orcid.org/0009-0000-5844-661X"
- family-names: "Lemson"
  given-names: "Gerard"
  affiliation: "Johns Hopkins University Scientific Software Engineering Center"
  orcid: "https://orcid.org/0000-0001-5041-2458"
- family-names: "Ling"
  given-names: "Jonathan P."
  affiliation: "Johns Hopkins School of Medicine"
  orcid: "https://orcid.org/0000-0003-1927-9729"
- family-names: "Maitland"
  given-names: "Iain"
  affiliation: "Johns Hopkins University Scientific Software Engineering Center"
  orcid: "https://orcid.org/0009-0008-3831-1927"
- family-names: "Mitschang"
  given-names: "Arik"
  affiliation: "Johns Hopkins University Scientific Software Engineering Center"
  orcid: "https://orcid.org/0000-0001-9239-012X"
- family-names: "Noss"
  given-names: "James"
  affiliation: "Johns Hopkins University Scientific Software Engineering Center"
  orcid: "https://orcid.org/0000-0002-0922-5770"
- family-names: "Sinha"
  given-names: "Irika R."
  orcid: "https://orcid.org/0000-0001-6440-7019"
  affiliation: "Johns Hopkins School of Medicine"
- family-names: "Wong"
  given-names: "Philip"
  affiliation: "Johns Hopkins School of Medicine"
  orcid: "https://orcid.org/0000-0001-8162-3274"

title: "SnapMine"
version: 1.0.0
doi: "10.5281/zenodo.13921401"
date-released: 2024-11-01
url: "https://github.com/ssec-jhu/snaptron_query"

GitHub Events

Total
  • Create event: 48
  • Release event: 3
  • Issues event: 17
  • Watch event: 1
  • Delete event: 33
  • Issue comment event: 65
  • Push event: 60
  • Pull request review comment event: 17
  • Pull request review event: 28
  • Pull request event: 79
Last Year
  • Create event: 48
  • Release event: 3
  • Issues event: 17
  • Watch event: 1
  • Delete event: 33
  • Issue comment event: 65
  • Push event: 60
  • Pull request review comment event: 17
  • Pull request review event: 28
  • Pull request event: 79

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 9
  • Total pull requests: 35
  • Average time to close issues: 11 days
  • Average time to close pull requests: 8 days
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 0.22
  • Average comments per pull request: 0.06
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 24
Past Year
  • Issues: 9
  • Pull requests: 35
  • Average time to close issues: 11 days
  • Average time to close pull requests: 8 days
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 0.22
  • Average comments per pull request: 0.06
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 24
View more stats
Top Authors
Issue Authors
  • irikas (9)
  • jamienoss (1)
  • fabbasinejad (1)
Pull Request Authors
  • dependabot[bot] (29)
  • fabbasinejad (9)
  • irikas (8)
Top Labels
Issue Labels
documentation (1)
Pull Request Labels
dependencies (29) python (27) remaining (1)

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • codecov/codecov-action v3 composite
  • docker/build-push-action f2a1d5e99d037542a71f64918e516c093c6f3fc4 composite
  • docker/login-action 65b78e6e13532edd9afa3aa52ac7964289d1a9c1 composite
  • docker/metadata-action 9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7 composite
.github/workflows/dist.yml actions
  • actions/checkout v4 composite
  • actions/download-artifact v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
.github/workflows/security.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
Dockerfile docker
  • python 3.11-slim build
pyproject.toml pypi
  • dash *
  • dash-ag-grid *
  • dash-bootstrap-components *
  • dash-bootstrap-templates *
  • dash-iconify *
  • dash-loading-spinners *
  • dash-mantine-components *
  • gunicorn *
  • httpx *
  • pandas *
requirements/all.txt pypi
requirements/build.txt pypi
  • build ==1.2.1
  • setuptools ==75.1.0
  • setuptools_scm ==8.1.0
requirements/dev.txt pypi
  • tox ==4.21.2 development
requirements/docs.txt pypi
  • nbsphinx ==0.9.3
  • sphinx ==7.3.7
  • sphinx-automodapi ==0.17.0
  • sphinx-issues ==4.1.0
  • sphinx_book_theme ==1.1.2
  • sphinx_rtd_theme ==2.0.0
requirements/prd.txt pypi
  • dash ==2.18.1
  • dash-ag-grid ==31.2.0
  • dash-bootstrap-components ==1.6.0
  • dash-bootstrap-templates ==1.2.4
  • dash-iconify ==0.1.2
  • dash-loading-spinners ==1.0.3
  • dash-mantine-components ==0.13.0.a3
  • gunicorn ==23.0.0
  • httpx ==0.27.0
  • pandas ==2.2.2
requirements/test.txt pypi
  • bandit ==1.7.9 test
  • pytest ==8.3.3 test
  • pytest-cov ==4.1.0 test
  • pytest-mock ==3.14.0 test
  • ruff ==0.6.5 test