pyMultiOmics
pyMultiOmics is a Python package for multi-omics data integration and analysis. It uses the Reactome database to map entities (genes, transcripts, proteins, compounds) to their reactions and pathways. The results is then shown as a network graph. Various analyses such as differential analysis, pathway activity analysis can be performed on this network graph, with the results overlaid on the graph.
Installation
Simply run:
pip install pyMultiOmics
Usage
Example basic usage is shown below:
from pyWebOmics.mapping import Mapper
species_name = DANIO_RERIO
m = Mapper(species_name) \
.set_gene(gene_data, gene_design) \
.set_protein(protein_data, protein_design) \
.set_compound(compound_data, compound_design) \
.build()
m contains a mapper object, which can be interogated to obtain the data integration results.
Please refer to this notebook for a demo.
Once mapping is completed, further analysis can be done. For example, finding DE entities:
from pyMultiOmics.analysis import AnalysisPipeline
ap = AnalysisPipeline(m)
method = INFERENCE_DESEQ
ap.run_de(method, GENES, 'Distal', 'Proximal')
ap.run_de(method, GENES, 'Distal', 'Middle')
ap.run_de(method, GENES, 'Proximal', 'Middle')
method = INFERENCE_LIMMA
ap.run_de(method, PROTEINS, 'Distal', 'Proximal')
ap.run_de(method, PROTEINS, 'Distal', 'Middle')
ap.run_de(method, PROTEINS, 'Proximal', 'Middle')
method = INFERENCE_T_TEST
ap.run_de(method, COMPOUNDS, 'Distal', 'Proximal')
ap.run_de(method, COMPOUNDS, 'Distal', 'Middle')
ap.run_de(method, COMPOUNDS, 'Proximal', 'Middle')
Various queries can now be performed on the pipeline:
- Retrieve a single node
from pyMultiOmics.query import QueryBuilder
node_id = '15366'
res = QueryBuilder(ap) \
.add(Entity(node_id)) \
.run()
res
- Retrieve multiple nodes
node_id = ['15366', 'ENSDARG00000037781', 'F1QAA7']
res = QueryBuilder(ap) \
.add(Entity(node_id)) \
.run()
res
- Retrieve nodes connected to a single node
query_id = 'F1QAA7'
res = QueryBuilder(ap) \
.add(Entity(query_id)) \
.add(Connected()) \
.run()
res
- Retrieve top-10 significantly changing genes
case = 'Distal'
control = 'Proximal'
pval = 0.05
fc_lte = -2
fc_gte = 2
N = 20
res = QueryBuilder(ap) \
.add(Select(GENES)) \
.add(SignificantDE(case, control, pval, fc_lte=fc_lte, fc_gte=fc_gte, N=N)) \
.run()
res
- Find the compounds that are connected to the DE genes above
res = QueryBuilder(ap) \
.add(Select(GENES)) \
.add(SignificantDE(case, control, pval, fc_lte=fc_lte, fc_gte=fc_gte, N=N)) \
.add(Connected(data_type=COMPOUNDS)) \
.run()
res
- Retrieve entity info
res = QueryBuilder(ap) \
.add(Select(GENES)) \
.add(SignificantDE(case, control, pval, fc_lte=fc_lte, fc_gte=fc_gte, N=N)) \
.add(Connected()) \
.add(Info()) \
.run()
res
