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ChipPy is ChIP-Seq with Python. It is a plotting and analysis tool for functional genomics.

It is written in Python (2.7) for the purpose of exploring the relationship between counts data, genomic positioning and gene expression. It relies on PyCogent, Ensembl andSQLite.

Both command-line and GUI interfaces are supported, in fact the GUI is built automatically from the command-line code so changes only need be made in one place. To use the GUI you will need to have PyQt4 installed on your system. To read ChIP-Seq reads directly from BAM files you will need to have Samtools installed.

Check out the latest updates to ChipPy

ChipPy works with a local database responsible for holding all genomic annotations and expression data. You'll need to either create one using the script start_chippy_db.py or (easier) downloading one. See Using ChipPy for more information.

ChipPy is divided between a core set of tools for plotting counts-based data relative to gene expression around annotated genomic sites:

add_expression_db.py - adds tabulated gene expression data to a ChipPy DB

drop_expression_db.py - removes a gene expression data set from a ChipPy DB

export_counts.py - retrieves counts data from a BAM, BED, BEDgraph, WIG or VCF file and saves it ready for plotting

plot_counts.py - creates plots from exported counts and gene expression data

calculate_periods.py - uses PyCogent's period analysis tools to look for repeating signals in exported data (coming soon!)

...and a set of additional tools for examining relationships within data sets:

diff_abs_plots.py - produces 'diamond' dot-plots of differential gene expression vs its absolute gene expression components

counts_distribution.py - looks at the distribution of counts values

expression_distribution.py - looks at the distribution of gene expression values

counts_vs_expr.py - various plots showing the relationship between counts and expression distributions

Citing ChipPy:

We are currenting preparing the ChipPy manuscript. For now, please just cite:

Jack, C.A., Pahwa, A., Huttley, G.A. (2014) ChipPy: An investigative tool for functional genomic relationships. The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.