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brisc

brisc is a high-performance library for analyzing single-cell data at scale. It prioritizes running as fast as possible on multi-core CPU systems, strict reproducibility, and a clean, user-friendly interface. On datasets of 1 to 20 million cells, it cuts the runtime of common workflows from hours to minutes.

Full documentation is available at brisc.run.

Why brisc?

  • Blazing fast — ground-up optimization of core algorithms and effective parallelism.
  • Deterministic — every step gives floating-point identical results between runs, regardless of the number of threads used.
  • Complete toolkit — preprocessing, dimensionality reduction, harmonization, label transfer, clustering, embedding, pseudobulk differential expression, and plotting.
  • Interoperable — reads and writes .h5ad, .rds, .h5Seurat, and 10x files, and supports interleaving Python and R analyses via ryp without intermediate writes to disk.
  • Memory-efficient — ~2× lower peak memory than Scanpy by tabulating which cells pass QC, instead of subsetting to them.
  • User-friendly — sensible defaults, strict type-checking, and solution-focused error messages.

Installation

brisc supports Linux, macOS, and Windows on Python 3.9+.

conda (recommended)

conda install -c conda-forge brisc

pip

pip install brisc

conda is recommended because it sets up the fast MKL BLAS and some of the R packages brisc uses. With pip, you'll need to handle those yourself: see the installation guide for details, including optional R integration (for differential expression, Seurat, and SingleCellExperiment support) via ryp.

Quick start

Basic workflow

from brisc import SingleCell

sc = SingleCell('data.h5ad')\
  .qc()\
  .hvg(batch_column='donor')\
  .normalize()\
  .pca()\
  .neighbors()\
  .shared_neighbors()\
  .cluster(resolution=[0.25, 0.5, 1, 1.5, 2])\
  .pacmap()

Label transfer

from brisc import SingleCell

sc_ref = SingleCell('data_ref.h5ad').qc()
sc_query = SingleCell('data_query.h5ad').qc()
sc_ref, sc_query = sc_ref.hvg(sc_query)
sc_ref = sc_ref.normalize()
sc_query = sc_query.normalize()
sc_ref, sc_query = sc_ref.pca(sc_query)
sc_ref, sc_query = sc_ref.harmonize(sc_query)
sc_query = sc_query.label_transfer_from(
  sc_ref, 'cell_type')

Pseudobulk differential expression

from brisc import SingleCell

pb = SingleCell('data.h5ad')\
  .qc()\
  .pseudobulk('sample', 'cell_type')
de = pb\
  .qc('condition')\
  .library_size()\
  .de('~ condition + sex + pmi')

Release files for brisc 0.1.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for brisc 0.1.2
File Size Uploaded
brisc-0.1.2.tar.gz 379.4 kB Details

Built distributions (wheels)

Table of built distributions (wheels) for brisc 0.1.2
File
brisc-0.1.2-cp314-cp314-win_amd64.whl CPython 3.14 CPython 3.14 Windows x86-64 Details
brisc-0.1.2-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.14 CPython 3.14 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
brisc-0.1.2-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.14 CPython 3.14 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
brisc-0.1.2-cp314-cp314-macosx_11_0_arm64.whl CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
brisc-0.1.2-cp314-cp314-macosx_10_15_x86_64.whl CPython 3.14 CPython 3.14 macOS 10.15+ x86-64 Details
brisc-0.1.2-cp313-cp313-win_amd64.whl CPython 3.13 CPython 3.13 Windows x86-64 Details
brisc-0.1.2-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.13 CPython 3.13 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
brisc-0.1.2-cp313-cp313-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.13 CPython 3.13 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
brisc-0.1.2-cp313-cp313-macosx_11_0_arm64.whl CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
brisc-0.1.2-cp313-cp313-macosx_10_13_x86_64.whl CPython 3.13 CPython 3.13 macOS 10.13+ x86-64 Details
brisc-0.1.2-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details
brisc-0.1.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 Details
brisc-0.1.2-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.12 CPython 3.12 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
brisc-0.1.2-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
brisc-0.1.2-cp312-cp312-macosx_10_13_x86_64.whl CPython 3.12 CPython 3.12 macOS 10.13+ x86-64 Details
brisc-0.1.2-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details
brisc-0.1.2-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
brisc-0.1.2-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.11 CPython 3.11 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
brisc-0.1.2-cp311-cp311-macosx_11_0_arm64.whl CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
brisc-0.1.2-cp311-cp311-macosx_10_9_x86_64.whl CPython 3.11 CPython 3.11 macOS 10.9+ x86-64 Details
brisc-0.1.2-cp310-cp310-win_amd64.whl CPython 3.10 CPython 3.10 Windows x86-64 Details
brisc-0.1.2-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.10 CPython 3.10 Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 Details
brisc-0.1.2-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.10 CPython 3.10 Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
brisc-0.1.2-cp310-cp310-macosx_11_0_arm64.whl CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
brisc-0.1.2-cp310-cp310-macosx_10_9_x86_64.whl CPython 3.10 CPython 3.10 macOS 10.9+ x86-64 Details
brisc-0.1.2-cp39-cp39-win_amd64.whl CPython 3.9 CPython 3.9 Windows x86-64 Details
brisc-0.1.2-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.9 CPython 3.9 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
brisc-0.1.2-cp39-cp39-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.9 CPython 3.9 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
brisc-0.1.2-cp39-cp39-macosx_11_0_arm64.whl CPython 3.9 CPython 3.9 macOS 11.0+ ARM64 Details
brisc-0.1.2-cp39-cp39-macosx_10_9_x86_64.whl CPython 3.9 CPython 3.9 macOS 10.9+ x86-64 Details

Total release size: 308.2 MB

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Release history Release notifications | RSS feed

0.1.6

31 release files

0.1.5

31 release files

0.1.4

31 release files

0.1.3

31 release files

This release

0.1.2 This release

31 release files

0.1.1

26 release files

0.1.0

26 release files

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