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.
  • 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

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:

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

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) yourself if you haven't used conda to do it:

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.