FracFixD v2.0.0 "Quokka"
FracFixD v2.0.0 "Quokka"
First public binary release of FracFixD, the native-D production sibling of the FracFixR R package for compositional analysis of fractionated RNA sequencing (polysome profiling, monosome / disome, subcellular fractionation, nuclear / cytoplasmic, RBP-IP, sucrose-gradient, and any other "split-into-fractions" RNA assay).
This release ships alongside FracFixR 1.1.0 (CRAN-ready R package, CC BY 4.0). FracFixR is the canonical scientific reference; FracFixD is its pipeline-scale binary sibling.
What's in this release
Single-binary executable that runs the GTK3 GUI by default and drops into headless CLI mode when called with --cli (or any subcommand). Built with LDC 1.42 (LLVM 21.1.8) + statically-linked D runtime + -O3 --flto=full -boundscheck=off.
Binary downloads
| File | Platform | Size | Notes |
|---|---|---|---|
fracfixd-linux-znver2-x86_64 |
Linux x86_64 | 8.0 MB | GUI + CLI; AMD Zen 2 / 3 / 4 (Ryzen 3000+, EPYC Rome / Milan / Genoa) |
fracfixd-linux-broadwell-x86_64 |
Linux x86_64 | 8.1 MB | GUI + CLI; Intel Broadwell or newer (i5 / i7 5th-gen+, Xeon E5 v4+) |
fracfixd-linux-generic-x86_64 |
Linux x86_64 | 8.1 MB | GUI + CLI; x86-64-v3 baseline (most 2013+ CPUs) |
fracfixd-cli-linux-x86_64-static |
Linux x86_64 | 1.8 MB | CLI only, no runtime deps beyond libc + libblas; ideal for containers and HPC node-locals |
FracFixD-2.0.0-macos-arm64.dmg |
macOS arm64 | 21 MB | Drag-to-Applications installer; native Mach-O launcher for Tahoe Gatekeeper |
fracfixd-2.0.0-macos-arm64.tar.gz |
macOS arm64 | 19 MB | Relocatable tree for CLI / pipeline use |
fracfixd-v2.0.0-windows-x86_64.zip |
Windows x86_64 | 38 MB | Portable ZIP; fracfixd.exe + GTK 3 + OpenBLAS + gfortran runtime closure (~70 DLLs) |
SHA256SUMS |
— | 1 KB | SHA-256 hashes for the seven artefacts above |
Verify your download:
# Linux / macOS
sha256sum -c SHA256SUMS
# Windows (PowerShell)
Get-FileHash *.zip,*.dmg,*-static,*-x86_64 -Algorithm SHA256Method highlights (carried forward unchanged)
- NNLS compositional fixup (plain / ridge / auto) — handles the "lost fraction" problem standard differential-expression tools (DESeq2, edgeR) can't.
- Seven differential-proportion test backends — GLM-LRT, binomial Wald, beta-binomial Wald, Rao score, HC0 / HC3 sandwich (optional cluster-robust), quasi-binomial.
- Multi-condition global LRT / joint Wald across K ≥ 2 conditions with optional per-pair contrasts.
- Three dispersion modes (global / trend / per-transcript) with optional Bayesian shrinkage prior on log-φ.
- Three FDR procedures (BH, BY, Storey q-values) + optional independent filtering.
- Three posterior log₂FC shrinkage estimators (normal, apeglm, ashr).
- Per-transcript permutation p-values with cluster-friendly deterministic seeding.
- Resumable pipeline via
--cache-fits/--from-cache(~10x faster re-runs). - Native FFXD1BIN proportions format (~30x faster than TSV to parse on 100k-transcript fixtures).
- Native SVG volcano plots with optional EnhancedVolcano-style R reproduction script export.
Equivalence
Default-flag output verified against FracFixR on every release via an in-tree equivalence harness: Spearman ρ(log₂FC) ≥ 0.99 and ρ(−log₁₀ p) ≥ 0.95 on the standard synthetic fixtures.
Documentation
- FracFixD README — install, quick start, full CLI reference
- FracFixD CHANGELOG
- BUILD_LINUX.md, BUILD_MACOS.md, BUILD_WINDOWS.md — per-platform source-build recipes
- BUILD_PROVENANCE.md — toolchain, flags, runtime-dep profile
Source code
The FracFixD D source code is closed and confidential under a separate licence held by Biocodecs / Arnaroo Ribologicals. Pre-compiled binaries are released under CC-BY-NC-ND-4.0. The complementary FracFixR R package (under CRAN/ in this repo) is fully open-source under CC BY 4.0 and is the right entry point for most academic users.
Citing
If you use FracFixR or FracFixD in research, please cite:
Cleynen A, Ravindran A, Shirokikh NE. FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data. Bioinformatics 42(2), February 2026, btaf615. https://doi.org/10.1093/bioinformatics/btaf615
Zenodo DOIs (auto-minted on release publication):
- Concept DOI (all versions, resolves to the latest): https://doi.org/10.5281/zenodo.20234583
- This release (v2.0.0 "Quokka"): https://doi.org/10.5281/zenodo.20307512