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libscran

C++ libraries for single-cell analysis
README.md

C++ libraries for single-cell analysis

This organization contains bits and pieces of C++ code for single-cell analysis. Most of this was originally taken from the scran R package, with some refactoring to enable re-use outside of R.

Developers can check out the scran-cli repository to see how the various libscran components fit together. For actual analyses, users are referred to the R, Python or Javascript bindings.

Popular repositories Loading

  1. umappp umappp Public

    C++ port of the UMAP algorithm

    C++ 75 15

  2. irlba irlba Public

    A C++ port of the IRLBA algorithm, based on the C code in the R package.

    C++ 17 4

  3. qdtsne qdtsne Public

    Quick-and-dirty t-SNE in C++

    C++ 11 3

  4. scran.chan scran.chan Public

    A slimmed down version of scran, based on the C++ library of the same name.

    R 10

  5. scranpy scranpy Public

    Single-cell data analysis, from C++ to Python

    Python 9

  6. scrapper scrapper Public

    R bindings to C++ code for single-cell analysis

    R 8

Repositories

Showing 10 of 35 repositories
  • scran_norm Public

    Normalize and log-transform count matrices

    libscran/scran_norm’s past year of commit activity
    C++ 0 MIT 0 0 0 Updated Apr 9, 2026
  • scran_markers Public

    Marker detection from single-cell expression data

    libscran/scran_markers’s past year of commit activity
    C++ 1 MIT 0 2 0 Updated Apr 8, 2026
  • scrapper Public

    R bindings to C++ code for single-cell analysis

    libscran/scrapper’s past year of commit activity
    R 8 0 4 0 Updated Apr 7, 2026
  • topicks Public

    Pick top genes for downstream analyses.

    libscran/topicks’s past year of commit activity
    C++ 2 MIT 0 0 0 Updated Apr 7, 2026
  • scran_qc Public

    Compute simple quality control metrics for each cell

    libscran/scran_qc’s past year of commit activity
    C++ 0 MIT 0 1 0 Updated Mar 26, 2026
  • scran_aggregate Public

    Aggregate expression values across groups of cells

    libscran/scran_aggregate’s past year of commit activity
    C++ 1 MIT 0 1 0 Updated Mar 26, 2026
  • scran_blocks Public

    Blocking utilities for libscran

    libscran/scran_blocks’s past year of commit activity
    C++ 0 MIT 0 0 0 Updated Mar 3, 2026
  • mnncorrect Public

    C++ implementation of the MNN correction algorithm

    libscran/mnncorrect’s past year of commit activity
    C++ 5 MIT 0 1 0 Updated Feb 27, 2026
  • irlba Public

    A C++ port of the IRLBA algorithm, based on the C code in the R package.

    libscran/irlba’s past year of commit activity
    C++ 17 MIT 4 3 1 Updated Feb 27, 2026
  • WeightedLowess Public

    A standalone C++ implementation of limma::weightedLowess.

    libscran/WeightedLowess’s past year of commit activity
    C++ 7 MIT 4 1 0 Updated Feb 27, 2026
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