subcellular_annotation

An annotation data frame for subcellular fractionation experiments
with nuclear and cytoplasmic fractions.

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

subcellular_annotation function

A data frame with 12 rows and 4 columns:<dl>
 <dt>Sample</dt>
<dd>Sample identifier</dd> <dt>Condition</dt>
<dd>Experimental condition (WT or Mutant)</dd> <dt>Type</dt>
<dd>Fraction type (Total, Nuclear, or Cytoplasmic)</dd> <dt>Replicate</dt>
<dd>Replicate identifier (Rep1 or Rep2)</dd>
</dl>

Format

Subcellular fractionation annotation example — subcellular_annotation

A data frame with 12 rows and 4 columns:<dl>
 <dt>Sample</dt>
<dd>Sample identifier</dd>

 <dt>Condition</dt>
<dd>Experimental condition (WT or Mutant)</dd>

 <dt>Type</dt>
<dd>Fraction type (Total, Nuclear, or Cytoplasmic)</dd>

 <dt>Replicate</dt>
<dd>Replicate identifier (Rep1 or Rep2)</dd>


</dl>

subcellular_annotation: Subcellular fractionation annotation example

Description

Usage

Arguments

Format

Examples