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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 713 177

  2. kb_python kb_python Public

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

    Python 182 27

  3. ffq ffq Public

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

    Python 592 47

  4. gget gget Public

    🧬 gget enables efficient querying of genomic reference databases

    Python 1.1k 81

  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 514 77

Repositories

Showing 10 of 168 repositories
  • monod Public

    The Monod package fits CME models to sequencing data.

    pachterlab/monod’s past year of commit activity
    Python 33 BSD-2-Clause 7 3 0 Updated Jan 14, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    pachterlab/gget’s past year of commit activity
    Python 1,094 BSD-2-Clause 81 20 3 Updated Jan 13, 2026
  • kb_python Public

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

    pachterlab/kb_python’s past year of commit activity
    Python 182 BSD-2-Clause 27 1 1 Updated Jan 12, 2026
  • SpatialFeatureExperiment Public

    Extension of SpatialExperiment with sf

    pachterlab/SpatialFeatureExperiment’s past year of commit activity
    R 56 Artistic-2.0 14 31 0 Updated Jan 11, 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 Jan 6, 2026
  • OP_2025_2 Public
    pachterlab/OP_2025_2’s past year of commit activity
    Jupyter Notebook 0 BSD-2-Clause 0 0 0 Updated Jan 6, 2026
  • varseek Public
    pachterlab/varseek’s past year of commit activity
    Python 16 BSD-2-Clause 0 1 0 Updated Jan 5, 2026
  • P_2026 Public

    Repository for the paper "Conditions for Evolution of Cooperation"

    pachterlab/P_2026’s past year of commit activity
    0 BSD-2-Clause 0 0 0 Updated Jan 4, 2026
  • BI-1C-2026 Public
    pachterlab/BI-1C-2026’s past year of commit activity
    1 BSD-2-Clause 0 0 0 Updated Dec 17, 2025
  • LP_2021 Public
    pachterlab/LP_2021’s past year of commit activity
    TeX 51 BSD-2-Clause 6 1 0 Updated Dec 15, 2025
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