Metadata-Version: 1.2
Name: Broad-GenePy
Version: 1.0
Summary: A useful module for any CompBio
Home-page: https://github.com/BroadInstitute/GenePy
Author: Jeremie Kalfon
Author-email: jkobject@gmail.com
License: UNKNOWN
Description: # GenePy
        
        _what is [genepy](https://en.wikipedia.org/wiki/G%C3%A9n%C3%A9pi)?_
        
        A set of awesome functions & tools for Computational Genomists
        
        ![long genome](documentation/genome.jpg)
        
        ## Content
        
        - **utils**: where a bunch of helper functions and usefull general scripts are stoed
          - **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, it contains a lot of functions required for the AML paper.
        
        ### 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**: 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 (WIP)
        
        `pip install GenePy`
        ### dev mode (better for now)
        
        ```bash
        git clone git://github.com/BroadInstitute/GenePy.git
        cd GenePy
        git submodule update --init
        ```
        
        then you can import files in python with e.g:
        ```python
        from GenePy import TerraFunction as terra
        ```
        
        if GenePy is not in your path, first do:
        
        ```python
        import sys
        sys.path.append(RELATIVE_PATH_TO_GenePy)
        ```
        
        now you can install the necessary python packages:
        
        ```bash
        pip install requirements.txt
        pip install rpy2-bioconductor-extensions gseapy macs2 deeptools
        ```
        
        or if not using the requirements.txt (computation results might change):
        
        ```bash
        pip install numpy pandas
        ```
        
        ```bash
        pip install bokeh dalmatian firecloud_dalmatian google_api_python_client gsheets gspread ipdb ipython matplotlib Pillow pybedtools pyBigWig pysam pytest requests rpy2 scikit_learn scipy seaborn setuptools taigapy taigapy typing venn rpy2-bioconductor-extensions gseapy macs2 deeptools
        ```
        
        then install the following tools:
        - [htslib/samtools](http://www.htslib.org/)
        - [bwa](https://github.com/lh3/bwa)
        just used once:
        - [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
        
        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"));'
        ```
        ## 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.
        
Platform: UNKNOWN
Requires-Python: >=3.5
