Science Score: 26.0%
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○Scientific vocabulary similarity
Low similarity (9.6%) to scientific vocabulary
Repository
Plotting tools for nanopore methylation data
Basic Info
Statistics
- Stars: 93
- Watchers: 7
- Forks: 13
- Open Issues: 12
- Releases: 0
Metadata Files
README.md
METHPLOTLIB
This script generates a browser view on a window using data from
i) nanopolish, either as methylation calls or methylation frequencies (as processed by calculatemethylationfrequency.py). The methylation calls can additionally be phased using scripts/annotatecallsbyphase.and scripts/splitcallsbyphase.py
ii) nanocompore
iii) in ont-cram format with MM/ML tags according to the SAM specifications
iv) in bedgraph format
INSTALLATION
Creating a new conda environment:
conda create -n methplotlib methplotlib
Or using pip:
pip install methplotlib
USAGE
``` methplotlib [-h] [-v] -m METHYLATION [METHYLATION ...] -n NAMES [NAMES ...] -w WINDOW [-g GTF] [-b BED] [-f FASTA] [--simplify] [--split] [--static STATIC] [--smooth SMOOTH] [--dotsize DOTSIZE] [--example] [-o OUTFILE] [-q QCFILE]
plotting nanopolish methylation calls or frequency
optional arguments: -h, --help show this help message and exit -v, --version Print version and exit. -m, --methylation METHYLATION [METHYLATION ...] data in nanopolish, nanocompore, ont-cram or bedgraph format -n, --names NAMES [NAMES ...] names of datasets in --methylation -w, --window WINDOW window (region) to which the visualisation has to be restricted -g, --gtf GTF add annotation based on a gtf file -b, --bed BED add annotation based on a bed file -f, --fasta FASTA required when --window is an entire chromosome, contig or transcript --simplify simplify annotation track to show genes rather than transcripts --split split, rather than overlay the methylation tracks --static Make a static image of the browser window (filename) --binary Make the nanopolish plot ignorning log likelihood nuances --smooth Rolling window size for averaging frequency values (int) --dotsize Control the size of dots in the per read plots (int) --example Show example command and exit. -o, --outfile OUTFILE File to write results to. Default: methylationbrowser{chr}{start}{end}.html. Use {region} as a shorthand for {chr}{start}{end} in the filename. Missing paths will be created. -q, --qcfile QCFILE File to write the qc report to. Default: The path in outfile prefixed with qc, default is qcreportmethyl ationbrowser{chr}{start}{end}.html. Use {region} as a shorthand for {chr}{start}_{end} in the filename. Missing paths will be created.
```
Snakemake workflow
For streamlining nanopolish a Snakefile is included (using snakemake). The workflow uses a config file, of which an example is in this repository.
Example data
The examples folder contains calls and frequencies for the human ACTB gene from PromethION sequencing of NA19240. An example command is available.
Companion scripts
The scripts folder contains scripts for phasing modification calls in haplotypes based on WhatsHap phasing, allele specific modification testing for phased data and differential modification testing across subjects.
TO DO - CONTRIBUTIONS WELCOME
- Outlier detection (in windows) across samples
Owner
- Name: Wouter De Coster
- Login: wdecoster
- Kind: user
- Location: Antwerp, Belgium
- Company: VIB-UAntwerp
- Website: https://gigabaseorgigabyte.wordpress.com/
- Twitter: wouter_decoster
- Repositories: 57
- Profile: https://github.com/wdecoster
Bioinformatics postdoc using short and long read sequencing in neurodegenerative disorders at Rademakers Lab
GitHub Events
Total
- Watch event: 4
- Issue comment event: 1
- Fork event: 1
Last Year
- Watch event: 4
- Issue comment event: 1
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| wdecoster | d****r@g****m | 261 |
| Endre Bakken Stovner | e****5@g****m | 24 |
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 40
- Total pull requests: 15
- Average time to close issues: 2 months
- Average time to close pull requests: 1 day
- Total issue authors: 26
- Total pull request authors: 2
- Average comments per issue: 5.5
- Average comments per pull request: 3.47
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- carolinehey (3)
- endrebak (3)
- Coracollar (3)
- JesseBNL (2)
- TaniaChP79 (2)
- Fatihlrcfs (2)
- dipannita-g (2)
- JoukjeKloosterman (2)
- clock-matt (2)
- sbecuwe (2)
- wdecoster (2)
- drkennetz (1)
- sarah872 (1)
- PaulaRomeroLozano (1)
- xiaohuli-45 (1)
Pull Request Authors
- wdecoster (11)
- endrebak (4)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 65 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 18
- Total maintainers: 1
pypi.org: methplotlib
Plot methylation data obtained from nanopolish
- Homepage: https://github.com/wdecoster/methplotlib
- Documentation: https://methplotlib.readthedocs.io/
- License: MIT
-
Latest release: 0.21.2
published about 2 years ago
Rankings
Maintainers (1)
Dependencies
- biopython *
- fisher >=0.1.9
- numpy >=1.16.5
- pandas >=0.23.4
- plotly >=4.9.0
- pyfaidx *
- pyranges >=0.0.77
- pysam *
- sklearn *