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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 775 186

  2. kb_python kb_python Public

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

    Python 194 31

  3. ffq ffq Public

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

    Python 606 49

  4. sleuth sleuth Public

    Differential analysis of RNA-Seq

    R 317 99

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

    Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

    Jupyter Notebook 554 78

  6. seqspec seqspec Public

    machine-readable file format for genomic library sequence and structure

    Python 130 21

Repositories

Showing 10 of 189 repositories
  • monod Public

    The Monod package fits CME models to sequencing data.

    pachterlab/monod's past year of commit activity
    Rust 37 BSD-2-Clause 7 3 0 Updated Nov 7, 2026
  • paperpush Public

    📝 Automated manuscript validation and submission portal completion

    pachterlab/paperpush's past year of commit activity
    Python 211 BSD-2-Clause 9 0 0 Updated Nov 7, 2026
  • OP_2025_2 Public
    pachterlab/OP_2025_2's past year of commit activity
    Jupyter Notebook 1 BSD-2-Clause 0 0 0 10BC8 Updated Nov 6, 2026
  • Manimble Public

    Edit manim slides

    pachterlab/Manimble's past year of commit activity
    Swift 5 BSD-2-Clause 0 0 0 Updated Nov 5, 2026
  • SpatialFeatureExperiment Public

    Extension of SpatialExperiment with sf

    pachterlab/SpatialFeatureExperiment's past year of commit activity
    R 59 Artistic-2.0 15 29 0 Updated Nov 4, 2026
  • seqspec Public

    machine-readable file format for genomic library sequence and structure

    pachterlab/seqspec's past year of commit activity
    Python 130 MIT 21 1 4 Updated Nov 3, 2026
  • cellsweep Public

    🧹 Remove technical noise from single-cell RNA sequencing count data with expectation-maximization

    pachterlab/cellsweep's past year of commit activity
    Jupyter Notebook 31 BSD-2-Clause 0 0 0 Updated Oct 30, 2026
  • RLSRP_2025 Public
    pachterlab/RLSRP_2025's past year of commit activity
    Jupyter Notebook 2 BSD-2-Clause 0 0 0 Updated Oct 28, 2026
  • rhopca Public
    pachterlab/rhopca's past year of commit activity
    Python 32 BSD-2-Clause 0 0 0 Updated Oct 28, 2026
  • edgePython Public

    Repository for edgePython which is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data.

    pachterlab/edgePython's past year of commit activity
    Python 104 GPL-3.0 9 0 0 Updated Oct 25, 2026
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