Broad-genepy 1.0

A useful module for any CompBio

# GenePy

_what is [genepy](https://en.wikipedia.org/wiki/G%C3%A9n%C3%A9pi)?_

A set of awesome functions & tools for Computational Genomists


## 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 [e-mail] [e-mail] https://jkobject.com

Apache license 2.0.