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@pachterlab

Pachter Lab

README.md

The Pachter Lab Github Organization

Open source software
  • concordex: Quantitative assessment of single-cell RNA-seq clustering (Python)
  • concordexR: Quantitative assessment of single-cell RNA-seq clustering (R)
  • ffq: Find sequencing data and metadata from public databases
  • gget: Efficient querying of genomic reference databases
  • k-spaces: Fit mixtures of low dimensional Gaussian latent variable models for data modeling, dimension reduction, and subspace learning
  • kallisto: Pseudoalignment for mapping sequence reads to targets, including quantification bulk and single-cell RNA-seq data
  • kb-python: Wrapper for the kallisto | bustools workflow for single-cell RNA-seq preprocessing
  • kite: Fast and accurate preprocessing of feature barcode experiments
  • metakallisto: metagenomics analysis with kallisto
  • monod: Fit chemical master equation models to sequencing data
  • PCCA: Couple PCA to CCA
  • rhoPCA: The ρPCA method for contrastive PCA of single-cell RNA-seq data
  • seqspec: A machine-readable YAML file format for genomic library sequence and structure
  • SpatialFeatureExperiment: Extension of SpatialExperiment with sf
  • sleuth: Differential analysis of bulk RNA-seq
  • splitcode: Flexible and efficient preprocessing, parsing, and manipulation of sequencing reads
  • qcbc: Quality control synthetic barcode sequences for orthogonal sequencing-based assays
  • voyager: Platform for exploratory spatial single-cell genomics data analysis
  • wompwomp: Make alluvial plots with node order and colors optimized to minimize edge crossings
Open source hardware
  • poseidon: Open source syringe pumps and microscope
  • colosseum: Open source fraction collector
Article repositories
These repositories contain code to reproduce figures and results from papers. Each repository has the naming convention [initials of author last names in order of appearance in the article]_[year published].

Pinned Loading

  1. kallisto kallisto Public

    Near-optimal RNA-Seq quantification

    C 722 178

  2. kb_python kb_python Public

    A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

    Python 183 28

  3. ffq ffq Public

    A tool to find sequencing data and metadata from public databases.

    Python 595 48

  4. gget gget Public

    🧬 gget enables efficient querying of genomic reference databases

    Python 1.1k 85

  5. sleuth sleuth Public

    Differential analysis of RNA-Seq

    R 312 96

  6. BI-BE-CS-183-2023 BI-BE-CS-183-2023 Public

    Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

    Jupyter Notebook 517 77

Repositories

Showing 10 of 169 repositories
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    pachterlab/gget’s past year of commit activity
    Python 1,099 BSD-2-Clause 85 21 1 Updated Feb 22, 2026
  • edgePython Public

    edgePython is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data. It also includes a new single-cell differential expression method that extends the NEBULA-LN negative binomial mixed model with edgeR's TMM normalization and empirical Bayes dispersion shrinkage.

    pachterlab/edgePython’s past year of commit activity
    Python 31 GPL-3.0 0 0 0 Updated Feb 21, 2026
  • gget_examples Public

    Examples for gget (https://github.com/pachterlab/gget).

    pachterlab/gget_examples’s past year of commit activity
    Jupyter Notebook 39 BSD-2-Clause 6 0 0 Updated Feb 20, 2026
  • SpatialFeatureExperiment Public

    Extension of SpatialExperiment with sf

    pachterlab/SpatialFeatureExperiment’s past year of commit activity
    R 57 Artistic-2.0 14 28 0 Updated Feb 19, 2026
  • cbrc-spec Public
    pachterlab/cbrc-spec’s past year of commit activity
    HTML 0 0 0 0 Updated Feb 17, 2026
  • 8cubeDB Public

    Query gene specificity in the founder mouse strains

    pachterlab/8cubeDB’s past year of commit activity
    Python 2 BSD-2-Clause 0 0 0 Updated Feb 12, 2026
  • voyager Public

    From geospatial to spatial -omics

    pachterlab/voyager’s past year of commit activity
    R 100 Artistic-2.0 14 22 0 Updated Feb 12, 2026
  • FCSKPP_2025 Public
    pachterlab/FCSKPP_2025’s past year of commit activity
    R 0 BSD-2-Clause 0 0 0 Updated Feb 9, 2026
  • seqspec Public

    machine-readable file format for genomic library sequence and structure

    pachterlab/seqspec’s past year of commit activity
    Python 128 MIT 18 1 2 Updated Feb 9, 2026
  • GP_2023 Public

    Switching processes

    pachterlab/GP_2023’s past year of commit activity
    Jupyter Notebook 0 BSD-2-Clause 0 0 0 Updated Feb 5, 2026
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