https://github.com/jkobject/genepy
A list of awesome files for computational biologists
https://github.com/jkobject/genepy
Last synced: 5 months ago
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A list of awesome files for computational biologists
- Host: GitHub
- URL: https://github.com/jkobject/genepy
- Owner: jkobject
- License: apache-2.0
- Created: 2019-05-14T18:15:37.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2024-01-26T16:28:11.000Z (over 2 years ago)
- Last Synced: 2026-01-13T17:25:08.227Z (5 months ago)
- Language: Python
- Homepage:
- Size: 23.8 MB
- Stars: 1
- Watchers: 1
- Forks: 8
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: HISTORY.md
- Contributing: CONTRIBUTING.md
- Funding: .github/FUNDING.yml
- License: LICENSE
Awesome Lists containing this project
README
[](https://zenodo.org/doi/10.5281/zenodo.10573223)
# genepy
_what is [genepy](https://en.wikipedia.org/wiki/G%C3%A9n%C3%A9pi)?_
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.
- **pyDESeq2**: it is a python integration of [deseq2]() (the differential expression analyser) with [rpy2]()
- **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)
- **cell_line_mapping-master/python/cell_line_mapper**: a set of functions to map cell line ids to other cell line ids based on an up to date google spreadsheet.
## Install
### with conda
```bash
conda create -n genepy python=3.9
conda activate genepy
conda install -c bioconda bioconductor-gsva
conda install -c bioconda bioconductor-deseq2
conda install -c bioconda bioconductor-gseabase
conda install -c bioconda bioconductor-erccdashboard
conda install -c bioconda samtools
conda install -c bioconda bwa
conda install -c bioconda bowtie2
conda install -c bioconda htslib
conda install -c bioconda bedtools
git clone git://github.com/BroadInstitute/genepy.git
cd genepy
pip install -e .
```
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
```
Some of the packages like gsheets, gcloud, firecloud-dalmatian will require you to create google accounts, login on your machine or download oauth files.
- [gcloud](https://cloud.google.com/sdk/docs/install-sdk)
- [firecloud-dalmatian](https://github.com/getzlab/dalmatian)
- [gsheets](https://github.com/xflr6/gsheets)
## 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.