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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 772 185

  2. kb_python kb_python Public

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

    Python 192 30

  3. ffq ffq Public

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

    Python 604 50

  4. sleuth sleuth Public

    Differential analysis of RNA-Seq

    R 316 98

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

    Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

    Jupyter Notebook 546 78

  6. seqspec seqspec Public

    machine-readable file format for genomic library sequence and structure

    Python 131 20

Repositories

Showing 10 of 184 repositories
  • paperpush Public
    pachterlab/paperpush's past year of commit activity
    Python 168 BSD-2-Clause 7 0 0 Updated Sep 12, 2026
  • cellsweep Public
    pachterlab/cellsweep's past year of commit activity
    Jupyter Notebook 28 BSD-2-Clause 0 0 0 Updated Sep 11, 2026
  • ctkit Public
    pachterlab/ctkit's past year of commit activity
    Python 2 BSD-2-Clause 0 0 0 Updated Sep 11, 2026
  • wompwomp Public
    pachterlab/wompwomp's past year of commit activity
    R 32 1 0 0 Updated Sep 10, 2026
  • HCP_2024 Public
    pachterlab/HCP_2024's past year of commit activity
    Jupyter Notebook 2 BSD-2-Clause 0 0 0 Updated Sep 9, 2026
  • wompywompy Public
    pachterlab/wompywompy's past year of commit activity
    Jupyter Notebook 3 0 0 0 Updated Sep 9, 2026
  • OP_2025 Public
    pachterlab/OP_2025's past year of commit activity
    Jupyter Notebook 1 BSD-2-Clause 0 0 0 Updated Sep 8, 2026
  • clrcycle Public
    pachterlab/clrcycle's past year of commit activity
    Jupyter Notebook 5 1 0 1 Updated Sep 8, 2026
  • attainable_information_figures Public

    Analysis code, figures, and manuscript for 'Image-Identifiable Genomic Subspaces: A Linear-Gaussian Model of Radiogenomic Recoverability'

    pachterlab/attainable_information_figures's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Sep 3, 2026
  • attainable_information Public
    pachterlab/attainable_information's past year of commit activity
    Python 2 MIT 0 0 0 Updated Sep 3, 2026
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