syntheticRNASeq 1.0.2

Generate synthetic RNA-Seq data by sampling a negative binomial distribution.

syntheticRNASeq

Introduction

syntheticRNASeq is a python package that allows generation of synthetic RNA-Sequencing data by sampling a negative binomial distribution. The output of the generators are pandas data frames with genes in rows and samples in columns.

Usage

Install and import the module:

!pip install syntheticRNASeq 
import syntheticRNASeq as synRNA
from syntheticRNASeq import SingleSampleGenerator, ReplicateGenerator, MultipleSampleGenerator #If you want to import specific class

Generation of a single sample

To create a single sample we will use the SingleSampleGenerator class and call the generate_single_sample function:

single_sample = SingleSampleGenerator(number_of_genes = 60_000,
									  neg_binomial_n = 0.5,
									  neg_binomial_p = 0.05,
									  seed = 0)
single_sample = single_sample.generate_single_sample()

Generation of a replicates from a single sample

To create triplicates from a single sample created from the above function we will use the ReplicateGenerator class and call the get_sample_replicates function:

replicates = ReplicateGenerator(normal_distribution_sigma = 1,
								df = single_sample,
								seed = 0)
replicates = replicates.get_sample_replicates()

Generation of multiple samples

To create multiple sample we will use the MultipleSampleGenerator class and call the generate_multiple_sample function:

multiple_samples = MultipleSampleGenerator(number_of_samples = 3,
										   number_of_genes = 60_000,
										   neg_binomial_n = 0.5,
										   neg_binomial_p = 0.05,
										   seed = 0)
multiple_samples = multiple_samples.generate_multiple_sample()

GitHub

https://github.com/ttkaralis/syntheticRNASeq