delanalysis 0.0.1

An analysis algoritm that is a companion to DEL-Decode

DEL-Analysis

DNA encoded library analysis. This is companion software to DEL-Decode for outputing analysis and graphs.

Table of Contents

• Installation
• Files Needed
• Methods
• Run

Installation

Anaconda python required for the instructions below

Download and move into directory

git clone https://github.com/Roco-scientist/DEL-Analysis.git
cd DEL-Analysis

Create a del environment

conda create -n del python=3
conda activate del
pip install -r requirements.txt

Build DEL-Analysis

python3 -m pip install --upgrade build
python3 -m build

Install DEL-Analysis

pip install ./dist/delanalysis-0.0.1-py3-none-any.whl

Files Needed

Output files from DEL-Decode

Methods

Work in progress

Merged data

Method	Description

Sample data

Method	Description

Run

Start

conda activate del
python

Working with merged data output

All code below is within python

import delanalysis

# Import merged data output from DEL-Decode.  This creates a DelDataMerged object
merged_data = delanalysis.read_merged("test_counts.all.csv")

# zscore, then quantile_normalize, then subtract background which is 'test_1'
merged_data_transformed = merged_data.zscore().quantile_normalize().subtract_background("test_1")

# Create a 2d comparison graph between 'test_2' and 'test_3' in the current directory and with a low end cutoff of 4
delanalysis.comparison_graph(merged_data_transformed, "test_2", "test_3", "./", 4)

# Creates a DelDataSample object from a single sample from the merged object
test_2_data_transformed = merged_data_transformed.sample_data("test_2")

# Create a 3d graph with each axis being a barcode within the current directory and a low end cutoff of 4
delanalysis.graph_3d(test_2_data_transformed, "./", 4)

# Create a 2d graph within the current directory and a low end cutoff of 4
delanalysis.graph_2d(test_2_data_transformed, "./", 4)

Working with sample data output

All code below is within python

import delanalysis

# Import sample data output from DEL-Decode.  This creates a DelDataSample object
sample_data = delanalysis.read_sample("test_1.csv")

# zscore
sample_data_zscore = sample_data.zscore()

# Create a 3d graph with each axis being a barcode within the current directory and a low end cutoff of 4
delanalysis.graph_3d(sample_data_zscore, "./", 4)

# Create a 2d graph within the current directory and a low end cutoff of 4
delanalysis.graph_2d(sample_data_zscore, "./", 4)