svist4get
A simple visualisation tool for genomic tracks from sequencing experiments.
Science Score: 49.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: scholar.google -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.0%) to scientific vocabulary
Keywords
Repository
A simple visualisation tool for genomic tracks from sequencing experiments.
Basic Info
Statistics
- Stars: 6
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Description
Svist4get is a simple bioinformatics tool for visualization of genomic signal tracks in user-defined genomic windows, either arbitrary selected by genomic coordinates or anchored to particular transcripts or genes.
Supported genomic signal tracks: bedGraph
Supported genome annotation: GTF (Ensembl or GENCODE)
Supported output: vector (pdf) and raster (png)
Programming language: Python 3
OS: Linux, Mac OS
Python dependencies: reportlab, statistics, biopython, configs, wand, argparse, pybedtools
OS-level dependencies: bedtools, ImageMagick (pdf-to-png conversion)
License: WTFPL
Version: 1.3.1 (July 2024)
Note: It's a new project's home page. It was moved from bitbucket: artegorov/svist4get. All new releases (starting with v. 1.3) of svist4get will be published only on this page (and pypi).
Installation
You need those tools at the OS level (probably installable as Linux packages): bedtools and ImageMagick (Ubuntu users, please consult FAQ regarding possible issues with ImageMagick).
- The most stable release of svist4get can be installed directly from pypi:
python3 -m pip install svist4get
- The development version is available at github :
git clone https://github.com/art-egorov/svist4get.git
cd svist4get
python3 -m pip install --upgrade pip
python3 -m pip install wheel
python3 setup.py sdist bdist_wheel
python3 -m pip install .
Contact
Please contact us by e-mail artemdotegorovATmeddotludotse or use Issues to report any technical problems.
Old Issues page from bitbucket.
Image example
Console commands to reproduce the above image
svist4get --sampledata
svist4get -bg svist4get_data/RiboCov_cut.bedGraph svist4get_data/mRNACov_cut.bedGraph -gtf svist4get_data/S.cerevisiae.gtf -fa svist4get_data/S.cerevisiae.dna.fa -bl Ribo-Seq RNA-Seq -w I 108842 113506 -it "CCR4 and FUN26 genes" -rc -c A4_p1
Reference
If you find svist4get useful, please cite:
Artyom A. Egorov, Ekaterina A. Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev and Ivan V. Kulakovskiy, svist4get: a simple visualization tool for genomic tracks from sequencing experiments, BMC Bioinformatics, Volume 20, 2019, 113, doi: 10.1186/s12859-019-2706-8
Detailed documentation
Quickstart guide
Command-line parameters
Configuration file parameters
API usage examples
FAQ
Version log
Known issues
Older versions of pybedtools (the necessary package) may fail to compile under Python 3.7. Usage of Python 3.6 is thus advised.
GTF annotations other than Ensembl and GENCODE may be parsed incorrectly in some cases. Usage of those annotation sources is advised.
pdf-to-png conversion may fail in some OS/ImageMagick combinations. Please consult FAQ for details.
Authors
svist4get is developed by Artyom Egorov at the Laboratory of Systems Biology of Aging, MSU (Current address: The Atkinson Lab, Department of Experimental Medical Science, Lund University). We are open for suggestions to extend and improve svist4get functionality. Please don't hesitate to share your ideas or feature requests.
*svist4get logo drawn by E. Kulakovskaya based on puppy named Cindy of S. Anisimova
Applications/Citations
More than 30 citations according to Google Scholar.
Owner
- Name: Artyom Egorov
- Login: art-egorov
- Kind: user
- Location: Lund, Sweden
- Company: Lund University
- Website: https://scholar.google.com/citations?user=r3VBTyoAAAAJ&hl=en
- Twitter: art_egorov
- Repositories: 2
- Profile: https://github.com/art-egorov
Bioinformatician at the Atkinson Lab, Department of Experimental Medical Science, Lund University
GitHub Events
Total
- Watch event: 2
Last Year
- Watch event: 2
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| art-egorov | a****v@m****e | 13 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 2
- Total pull requests: 0
- Average time to close issues: 1 day
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 2.5
- 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
Top Authors
Issue Authors
- aowenson-imm (1)
- losuler (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 184 last-month
- Total dependent packages: 1
- Total dependent repositories: 1
- Total versions: 48
- Total maintainers: 1
pypi.org: svist4get
A simple visualization tool for genomic tracks from sequencing experiments
- Homepage: https://github.com/art-egorov/svist4get
- Documentation: https://svist4get.readthedocs.io/
- License: WTFPL
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Latest release: 1.3.1
published over 3 years ago
Rankings
Maintainers (1)
Dependencies
- Pybedtools *
- argparse *
- biopython *
- configs *
- reportlab *
- statistics *
- wand *