This notebook contains instructions for the submission of BioJupies RNA-seq data analysis plugins in Python 3.
To submit your plugin, complete the following three steps:
analyze
function.plot
function.analyze
¶The goal of the analyze
function is to analyze an RNA-seq dataset or signature using one or more computational tools or techniques, and return the results of such analysis in a Python data structure.
# Analysis function
def analyze(dataset):
print('Analyzing the dataset...')
return ''
plot
¶The goal of the plot
function is to visualize the results of the analyze
function in the Jupyter Notebook by using a plot, interactive visualization, or embedding downloadable results in the notebook itself.
# Plot function
def plot(analysis_results):
print('Displaying analysis results...')
Once the analyze
and plot
functions have been completed, you can test them using the cells below.
# Import modules
import pandas as pd
# Read the dataset
example_dataset = pd.read_table('data/example_dataset.txt', index_col='gene_symbol')
# Read the metadata
example_metadata = pd.read_table('data/example_metadata.txt', index_col='Sample_geo_accession')
# Read the signature
example_signature = pd.read_table('data/example_signature.txt', index_col='gene_symbol')
# Analyze the data
results = analyze(dataset=example_dataset)
Analyzing the dataset...
# Plot the results
plot(results)
Displaying analysis results...