FracFixR / FracFixD

Overview

A compositional statistical framework for estimating absolute proportions between fractions in RNA-seq experiments, correcting the biases that arise in polysome profiling and sucrose-gradient fractionation. FracFixR is the open-source R reference implementation; FracFixD is the high-performance native-D sibling, a single executable with GUI and CLI for cluster and pipeline use.

Linux · macOS · Windows · R: CC-BY-4.0 / D binaries: CC-BY-NC-ND-4.0

Quick start

devtools::install_github("Arnaroo/FracFixR/CRAN")
library(FracFixR)

curl -fsSL https://github.com/Arnaroo/FracFixR/releases/download/fracfixd-v2.0.6/fracfixd-linux-znver2-x86_64 \
  -o /usr/local/bin/fracfixd && chmod +x /usr/local/bin/fracfixd
fracfixd --help

The problem it solves

In fractionated RNA-seq experiments the original proportions between fractions are obscured by library preparation and by differences in sequencing depth, and some material is unrecoverable during fractionation. Standard tools such as DESeq2 and edgeR are inappropriate because they assume independent samples, cannot estimate the unobserved lost fraction, and do not account for the compositional nature of the data, where fractions are parts of a whole.

How it works

FracFixR models whole-cell RNA as a non-negative linear combination of its fractions plus an intercept that represents the lost, unrecoverable fraction. It selects informative transcripts, fits a non-negative least squares regression to estimate fraction weights, recovers individual transcript proportions in each fraction, corrects counts for library-size differences, and performs differential proportion testing between conditions.

Two implementations

• FracFixR: the open R reference (CC-BY-4.0), the right entry point for interactive academic analysis. Install with devtools::install_github("Arnaroo/FracFixR/CRAN").
• FracFixD: the production binary sibling in native D (CC-BY-NC-ND-4.0), a single executable with GUI and CLI for cluster, Snakemake and Nextflow workflows, shipped for Linux, macOS and Windows.
• Works with any RNA fractionation protocol: polysome profiling, subcellular localisation, nuclear-cytoplasmic fractionation, and RNA-protein complex isolation.