CLI Guide | Core API Guide | Zea Eureka
JanusX (Joint Association and Novel Utility for Selection) is a GWAS and genomic selection toolkit that combines:
- Rust-accelerated kernels (PyO3 extension)
- Python analysis modules
- A Rust launcher (
jx) for runtime/toolchain management and pipeline orchestration
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\____/ \__,_|_| |_|\__,_|___/_/ \_\ Tools for GWAS and GS
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Main capabilities:
- Genome-Wide Association Study (GWAS):
lm,lmm,lmm2,fvlmm, SparseLMM (splmm/splmm-exact), andfarmcpu - Genomic Selection (GS):
BLUP,BayesA/B/C/R, and ML models (RF/ET/GBDT/XGB/SVM/ENET) - Streaming genotype IO for VCF/HMP/PLINK
- Post-analysis workflows:
postgwas,postgs - Utility workflows:
grm,pca,gformat,gmerge,fastpop
- Linux | MacOS
curl -fsSL https://raw.githubusercontent.com/FJingxian/JanusX/main/scripts/install.sh | sh- Windows
powershell -ExecutionPolicy ByPass -c "irm https://raw.githubusercontent.com/FJingxian/JanusX/main/scripts/install.ps1 | iex"pip install janusxconda create -n janusx \
--channel conda-forge \
--channel bioconda \
janusx# Estimate variance for every SNP.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -lmm -o test/
# Exact LMM with Wald and likelihood-ratio results.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -lmm2 -o test/
# Estimate variance once in NULL model, similar with EMMAX. (fast, recommend)
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -fvlmm -o test/
# SparseLMM with sparse REML null and approximate GRAMMAR-gamma scan.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -splmm -o test/
# SparseLMM with the exact sparse-Cholesky g'Pg scan denominator.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -splmm-exact -o test/
# FarmCPU.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -farmcpu -o test/
jx postgwas -i test/mouse_hs1940.test0.lmm.tsv -manh -qq -thr 1e-6 -o testpost/
jx postgwas -i test/mouse_hs1940.test0.lmm.tsv test/mouse_hs1940.test1.lmm.tsv -manh-merge -qq-merge -fontsize 11 -fontstyle arial -o testpost/
jx postgwas -i test/mouse_hs1940.test0.lmm.tsv test/mouse_hs1940.test1.lmm.tsv test/mouse_hs1940.test2.lmm.tsv -manh-merge -qq-merge -scatter-size 4 10 -alpha 0.2 0.5 -ylim 2 10 -o testpost/
# BLUP method, prepared for biobank cohorts
# n≤15,000 GBLUP
# n>15,000 & m≤15,000 rrBLUP
# n>15,000 & m>15,000 rrBLUP with PCG (Jacobi)
jx gs -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -BLUP -o test/ -cv 5
# Bayesian methods (BayesR in JanusX-2.0.0 uses pi=(0.95,0.03,0.01,0.01), gamma=(0,0.01,0.1,1))
jx gs -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -BayesA -BayesB -BayesC -BayesR -o test/ -cv 5
# BayesB fixes pi at 0.05 by default; append a value to override it. BayesC
# estimates pi unless a value is supplied:
# jx gs ... -BayesB 0.05 -BayesC 0.10* Genomic Selection for trait: test0
Train size: 1410, Test size: 530, EffSNPs: 8960
** BLUP
✔︎ Cross-validation ...Finished [0.8s]
✔︎ Fitting ...Finished [0.3s]
✔︎ Predicting ...Finished [0.0s]
** BayesA
✔︎ Cross-validation ...Finished [17.9s]
✔︎ Fitting ...Finished [4.1s]
✔︎ Predicting ...Finished [0.0s]
...
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Fold Method Pearsonr Spearmanr R2 time(s) Best
1 BLUP 0.704 0.675 0.493 0.198
1 BayesA 0.709 0.680 0.493 3.507
...
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jx -h
jx <module> -hSee full usages in CLI Guide.
Genome-wide Association Studies (GWAS):
grmpcagwaspostgwas(Visualization,manhqqldblock)fastpop(population-structure analysis)
Attribution note:
- FastPop is JanusX's own population-structure workflow and public name for this module.
- Historical JanusX releases referenced ADAMIXTURE as a related implementation; the BSD-3-Clause attribution notice is recorded in THIRD_PARTY_NOTICES.md.
Genomic Selection (GS):
gspostgs(Visualization)
Epistasis:
garfield(Based on https://github.com/heroalone/Garfield)
Utility:
gformat(Conversion between genotype data formats, support fast splicing/filtering/prune)gmerge(Merge genotype between samples)gstats(State freq/het/missing/ldscore of genotype)
@article{FuJanusX,
author = {Fu, Jingxian and Jia, Anqiang and Wang, Haiyang and Liu, Hai-Jun},
title = {JanusX: an integrated and high-performance platform for scalable genome-wide association studies and genomic selection},
journal = {The Plant Journal},
volume = {127},
number = {5},
pages = {e71105},
doi = {https://doi.org/10.1111/tpj.71105},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.71105},
year = {2026}
}This project is licensed under GNU Affero General Public License v3.0 (AGPL-3.0-or-later). See LICENSE.