Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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○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 (8.5%) to scientific vocabulary
Keywords
Repository
Generate heatmap plots from genomic BigWig data
Basic Info
Statistics
- Stars: 2
- Watchers: 0
- Forks: 0
- Open Issues: 2
- Releases: 0
Topics
Metadata Files
README.md
Wigman documentation
Generate heatmap files from BigWig data.
Example
Run the script:
In order to run the plotting script, you need a config "instruction" file. The file
should look like the following template:
Bed/Wig/pdf filename min max step colormap title description
My config.txt contains the following:
bed hg19/tata_plus.bed 50 50 TATA-Plus
bed hg19/tata_minus.bed 50 50 TATA-Minus
bw hg19.100way.phyloP100way.bw -4 4.02 2 BuRd PhyloP Conservation Score
bw hg19.100way.phastCons.bw 0 1.02 0.5 Reds PhastCons Element Conservation
bw ENCFF000SLA.bigWig 0 50.2 25 Hot K562 Base Overlap Signal
bw ENCFF000SPQ.bigWig 0 20.2 10 Hot HeLa Base Overlap Signal
bw GSM1480321_K562_GROcap_wTAP_plus.bigWig 0 10.2 5 Reds Plus Read
bw GSM1480321_K562_GROcap_wTAP_minus.bigWig -10 0.5 5 Blues Minus Read
pdf tata_profile.png size
Then run the following command:
main.py config.txt
Citations
If this software was helpful please consider citing it with:
Mahpour A, Scruggs BS, Smiraglia D, Ouchi T, Gelman IH (2018) A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters. PLOS ONE 13(10): e0205608. https://doi.org/10.1371/journal.pone.0205608
Owner
- Name: Amin Mahpour
- Login: AminMahpour
- Kind: user
- Location: Boston, MA
- Website: aminmahpour.com
- Twitter: Kavoshex
- Repositories: 12
- Profile: https://github.com/AminMahpour
Amin is a biochemist and Computational Biologist.
GitHub Events
Total
Last Year
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 46
- Total Committers: 3
- Avg Commits per committer: 15.333
- Development Distribution Score (DDS): 0.413
Top Committers
| Name | Commits | |
|---|---|---|
| Amin Mahpour | a****r@A****l | 27 |
| t8jtw1 | @l****6 | 15 |
| Amin Mahpour | A****r@u****m | 4 |
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 0
- Total pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: 4 days
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.33
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 3
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
Pull Request Authors
- dependabot[bot] (3)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 8 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 1
- Total maintainers: 1
pypi.org: wigman
A package to plot genomic scores
- Homepage: https://github.com/AminMahpour/Wigman
- Documentation: https://wigman.readthedocs.io/
- License: GNU General Public License v2 (GPLv2)
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Latest release: 1.0.0
published over 6 years ago
Rankings
Maintainers (1)
Dependencies
- matplotlib ==2.0.0
- numpy ==1.11.3
- pyBigWig ==0.3.3
- tqdm ==4.11.2