marlenfafouti/brisc repository overview

⁠brisc

Single-cell differential expression container bridging Python (brisc) and R (limma/edgeR) via ryp. Built on Bioconductor for cross-platform (amd64) HPC deployment via Apptainer/Singularity.

⁠Tags

• bioc-v2-mkl (current) — numpy/scipy linked against Intel MKL, required for brisc's fast path (NN search, harmonization, label transfer).
• bioc-v1 (legacy) — OpenBLAS; slower, no fast path.

⁠Contents

-Base:bioconductor/bioconductor_docker:RELEASE_3_20 (R 4.4.x, Bioconductor 3.20)

• Python 3.12 (conda-forge): numpy, scipy (MKL-linked), anndata,polars, pandas, pyarrow, h5py, threadpoolctl
• brisc==0.1.5, ryp (pip)
• R: limma, edgeR, arrow (required by ryp for R-Python transfer)

⁠Usage

apptainer pull brisc_bioc-v2-mkl.sif docker://marlenfafouti/brisc:bioc-v2-mkl
  
Check BLAS backend:

apptainer exec brisc_bioc-v2-mkl.sif python -c \
"from threadpoolctl import threadpool_info; 
print(sorted({p['internal_api'] for p in threadpool_info()}))"
# expect: ['mkl', 'openmp']