example_counts

A matrix containing simulated RNA-seq counts for 100 genes across 12 samples.
The data simulates a polysome profiling experiment with two conditions
(Control and Treatment) and three fractions (Total, Light_Polysome, Heavy_Polysome).

datasets

A compositional statistical framework for absolute proportion
estimation between fractions in RNA sequencing data. 'FracFixR' addresses
the fundamental challenge in fractionated RNA-seq experiments where library
preparation and sequencing depth obscure the original proportions of RNA
fractions. It reconstructs original fraction proportions using non-negative
linear regression, estimates the "lost" unrecoverable fraction, corrects
individual transcript frequencies, and performs differential proportion
testing between conditions. Supports any RNA fractionation protocol including
polysome profiling, sub-cellular localization, and RNA-protein complex isolation.

Alice Cleynen

FracFixR

Compositional Statistical Framework for RNA Fractionation
Analysis

Agin Ravindran

Nikolay Shirokikh

example_counts function

A numeric matrix with 100 rows (genes) and 12 columns (samples):<dl>
 <dt>rows</dt>
<dd>Gene identifiers (Gene1 to Gene100)</dd> <dt>columns</dt>
<dd>Sample identifiers (Sample1 to Sample12)</dd>
</dl>

Format

Example RNA-seq count matrix — example_counts

A numeric matrix with 100 rows (genes) and 12 columns (samples):<dl>
 <dt>rows</dt>
<dd>Gene identifiers (Gene1 to Gene100)</dd>

 <dt>columns</dt>
<dd>Sample identifiers (Sample1 to Sample12)</dd>


</dl>

example_counts: Example RNA-seq count matrix

Description

Usage

Arguments

Format

Examples