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    49 repositories

    • cellAdmix-core

      Public
      core cellAdmix algorithm implementation in C++ with R and python bindings
      C++
      •
      MIT License
      •0•3•0•2•Updated Oct 21, 2026Oct 21, 2026

    • cacoa

      Public
      Single-cell Case Control Analysis
      R
      •12•59•11•1•Updated Oct 13, 2026Oct 13, 2026

    • Baysor

      Public
      Bayesian Segmentation of Spatial Transcriptomics Data
      segmentationbayesianspatial-transcriptomics
      segmentationbayesianspatial-transcriptomicsxenium
      C++
      •
      MIT License
      •43•219•1•0•Updated Oct 2, 2026Oct 2, 2026

    • aba

      Public
      A Bioinformatics Agency
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 15, 2026Sep 15, 2026

    • weft

      Public
      Easy management of remote compute and environments for data analytics agents
      pixikernelsagents
      pixikernelsagentsenvironmentsremote-computeijupyter
      Python
      •0•0•0•0•Updated Sep 10, 2026Sep 10, 2026

    • clone2vec

      Public
      Repository for the clone2vec python package
      Python
      •1•26•0•0•Updated Sep 8, 2026Sep 8, 2026

    • weft-ui

      Public
      Reference UI for weft: data analytics with remote compute and environments made easy!
      pixidata-analysisenvironments
      pixidata-analysisenvironmentsremote-computeijupyter
      TypeScript
      •0•0•0•0•Updated Aug 9, 2026Aug 9, 2026

    • pagoda3

      Public
      A generative UI scRNA-seq viewer for lstar files in pagoda3 style: exploration, analysis, annotation
      TypeScript
      •
      MIT License
      •0•1•0•0•Updated Jul 31, 2026Jul 31, 2026

    • lstar

      Public
      L* - a universal single-cell and spatial transcriptomics representation and storage schema
      C++
      •
      MIT License
      •0•3•0•0•Updated Jul 30, 2026Jul 30, 2026

    • aba-recipe-pack

      Public
      Standard ABA bioinformatics cookbook — hand-curated recipes + biomni-derived recipes (Apache 2.0). Layered content overlay for the ABA platform.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 27, 2026Jul 27, 2026

    • libzarr

      Public
      Header-only C++17 library for reading and writing Zarr v2 and v3 — sharding, ZIP archives, WASM-compatible, zero-dependency core.
      cppwebassemblyfile-format
      cppwebassemblyfile-formatscientific-computingheader-onlycpp17ndarrayzarrome-zarr
      C++
      •
      MIT License
      •0•1•0•0•Updated Jul 8, 2026Jul 8, 2026

    • conos

      Public
      R package for the joint analysis of multiple single-cell RNA-seq datasets
      scrna-seqsingle-cell-rna-seqbatch-correction
      scrna-seqsingle-cell-rna-seqbatch-correction
      R
      •
      GNU General Public License v3.0
      •40•233•8•2•Updated Jul 2, 2026Jul 2, 2026

    • pagoda2

      Public
      R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
      scrna-seqtranscriptomicssingle-cell
      scrna-seqtranscriptomicssingle-cellsingle-cell-rna-seq
      JavaScript
      •46•261•2•0•Updated Jun 28, 2026Jun 28, 2026

    • aba-bundle-starter

      Public
      Template for ABA-compatible agent bundles (institution / lab / user scopes). See README for layering rules and authoring guide.
      Shell
      •0•0•0•0•Updated Jun 22, 2026Jun 22, 2026

    • sccore

      Public
      Core utilities for single-cell RNA-seq
      R
      •3•13•0•0•Updated Jun 16, 2026Jun 16, 2026

    • N2R

      Public
      R extensions to N2 implementing approximate nearest neighbor search methods
      C++
      •3•10•1•1•Updated Jun 14, 2026Jun 14, 2026

    • leidenAlg

      Public
      Implements the Leiden algorithm via an R interface
      C
      •4•13•1•0•Updated May 31, 2026May 31, 2026

    • xeSim

      Public
      Combines physical models with neural net rendering to learn the biology in Xenium datasets
      Python
      •0•3•0•0•Updated May 22, 2026May 22, 2026

    • clone2vec_analysis

      Public
      Code accompanying the clone2vec manuscript
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Apr 26, 2026Apr 26, 2026

    • scistreer

      Public
      R/Rcpp implementation of the ScisTree algorithm
      evolutionphylogeneticssingle-cell
      evolutionphylogeneticssingle-cell
      R
      •
      GNU General Public License v3.0
      •3•9•0•0•Updated Feb 4, 2026Feb 4, 2026

    • numbat

      Public
      Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
      cancer-genomicssingle-cellphylogeny
      cancer-genomicssingle-cellphylogenysingle-cell-rna-seqsingle-cell-analysissingle-cell-atac-seqcnv-detectionsingle-cell-omicsspatial-transcriptomicslineage-tracing
      R
      •
      Other
      •35•232•79•1•Updated Feb 4, 2026Feb 4, 2026

    • cellAdmix

      Public
      Jupyter Notebook
      •
      MIT License
      •6•39•10•7•Updated Jan 22, 2026Jan 22, 2026

    • thymus-mesenchyme

      Public
      Code and notebooks for Gustafsson et al. scRNA-Seq analysis of thymic mesenchymal cells
      Jupyter Notebook
      •0•1•1•0•Updated Nov 5, 2025Nov 5, 2025

    • clonal-atlas-paper

      Public
      The repository with the code and analysis for the paper [Erickson et al]
      Jupyter Notebook
      •0•3•0•0•Updated Jun 5, 2025Jun 5, 2025

    • cellAdmix-Notebooks

      Public
      Jupyter Notebook
      •
      MIT License
      •0•7•2•0•Updated Apr 23, 2025Apr 23, 2025

    • GraphPriorKMeans

      Public
      Julia
      •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • cellAdmix-preprint

      Public
      Evaluating and correcting cell admixtures in imaging-based spatial transcriptomics data
      Jupyter Notebook
      •
      Other
      •2•1•1•0•Updated Sep 25, 2024Sep 25, 2024

    • gpsFISH

      Public
      Optimization of gene panels for targeted spatial transcriptomics
      R
      •
      Other
      •2•7•3•0•Updated Jul 16, 2024Jul 16, 2024

    • scITD

      Public
      Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
      R
      •4•68•8•0•Updated Apr 14, 2024Apr 14, 2024

    • hahmmr

      Public
      Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq
      R
      •
      Other
      •0•13•2•0•Updated Apr 2, 2024Apr 2, 2024
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