what is genepy?
A set of awesome functions & tools for Computational Geneticists
- 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.
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.
pip install broad-genepy
and then use with from genepy.utils/epigenetics/... import ...
git clone git://github.com/BroadInstitute/genepy.git
pip install -e genepy
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
hg38 genome sizes: from https://github.com/igvteam/igv/blob/master/genomes/sizes/hg38.chrom.sizes
Install the following tools:
- htslib/samtools
- bwa just used once:
- bowtie2
Finaly you can install R packages (GSEABase, erccdashboard, GSVA, DESeq2):
R -e 'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")};BiocManager::install(c("GSEABase", "erccdashboard", "GSVA", "DESeq2"));'
please do contribute, we do not have time to fix all issues or work on feature requests
Jeremie Kalfon [email protected] [email protected] https://jkobject.com
Javad Noorbakhsh [email protected]
Apache license 2.0.