https://github.com/broadinstitute/genepy
Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python
Science Score: 10.0%
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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
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○Academic publication links
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✓Committers with academic emails
3 of 6 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.0%) to scientific vocabulary
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Repository
Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python
Basic Info
- Host: GitHub
- Owner: broadinstitute
- License: apache-2.0
- Language: Python
- Default Branch: master
- Homepage: https://pypi.org/project/Broad-genepy/
- Size: 23.9 MB
Statistics
- Stars: 21
- Watchers: 2
- Forks: 5
- Open Issues: 2
- Releases: 0
Topics
Metadata Files
README.md
genepy
what is genepy?
A set of awesome functions & tools for Computational Geneticists
Content
- utils: where a bunch of helper functions and usefull general scripts are stored
- plots: a set of plotting tools based on matplotlib and bokeh to make volcano plots / CNV maps etc..
- helper: and additional helper functions to save data, do merging of dataframes...
- terra: contains a set of functions that uses dalmatian to interact with the GCP powered genomics HPC platform: Terra.
- sequencing: contains a set of function to works with bed/bam/fastqs...
- rna: contains function to work with RNAseq (and related) data.
- mutations: a set of functions to work with maf files, vcf files etc..
- google: functions and packages linked to google's apis
- google_sheet: function to upload a df as a google sheet
- gcp: sets of functions to interact with google storage (relies on
gsutil)
- epigenetics: where we have things related to epigenomics
- chipseq: has functions to read, merge, denoise, ChIP seq data.
- plot: has functions to plot ChIP seq data.
Helper tools
tools that you do not need to use directly as they have binding functions in genepy.
- epigenetics/rose:: where an updated version of the rose algorithm is stored (as a git submodule)
- celllinemapping-master/python/celllinemapper: a set of functions to map cell line ids to other cell line ids based on an up to date google spreadsheet.
Install
with pip
pip install broad-genepy
and then use with from genepy.utils/epigenetics/... import ...
Please see the next step to get access to all bindings and tools.
dev mode
bash
git clone git://github.com/BroadInstitute/genepy.git
pip install -e genepy
then you can import files in python with e.g: ```python from genepy import terra from genepy.utils import helper as h from genepy.google import gcp from genepy.utils import plot from genepy.epigenetics import chipseq
```
installation: to get access to all bindings and tools
Install the following tools: - gcloud - firecloud-dalmatian - gsheets - htslib/samtools - bwa just used once: - bowtie2
Some of these packages like gsheets, gcloud, firecloud-dalmatian will require you to create google accounts, login on your machine or download oauth files.
Finaly you can install R packages (GSEABase, erccdashboard, GSVA, DESeq2):
bash
R -e 'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")};BiocManager::install(c("GSEABase", "erccdashboard", "GSVA", "DESeq2"));'
data:
hg38 genome sizes: from https://github.com/igvteam/igv/blob/master/genomes/sizes/hg38.chrom.sizes
About
please do contribute, we do not have time to fix all issues or work on feature requests
Jeremie Kalfon jkalfon@broadinstitute.org jkobject@gmail.com https://jkobject.com
Apache license 2.0.
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 360
- Total Committers: 6
- Avg Commits per committer: 60.0
- Development Distribution Score (DDS): 0.117
Top Committers
| Name | Commits | |
|---|---|---|
| jkobject | j****t@g****m | 318 |
| Javad Noorbakhsh | j****k@b****g | 16 |
| Gwen Miller | g****r@b****g | 15 |
| monikaperez | m****z@g****m | 5 |
| Simone Zhang | x****g@b****g | 4 |
| dependabot[bot] | 4****]@u****m | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 0
- Total pull requests: 21
- Average time to close issues: N/A
- Average time to close pull requests: 11 days
- Total issue authors: 0
- Total pull request authors: 7
- Average comments per issue: 0
- Average comments per pull request: 0.48
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 1
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
- javadnoorb (8)
- jkobject (7)
- monikaperez (1)
- dependabot[bot] (1)
- qinqian (1)
- XL-whitelabgx (1)
- 5im1z (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 51 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 11
- Total maintainers: 1
pypi.org: broad-genepy
A useful module for any CompBio
- Homepage: https://github.com/BroadInstitute/genepy
- Documentation: https://broad-genepy.readthedocs.io/
- License: apache-2.0
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Latest release: 1.2.6
published over 3 years ago