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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
  • 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
  • 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
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 706 177

  2. kb_python kb_python Public

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

    Python 174 28

  3. ffq ffq Public

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

    Python 592 48

  4. gget gget Public

    🧬 gget enables efficient querying of genomic reference databases

    Python 1.1k 78

  5. sleuth sleuth Public

    Differential analysis of RNA-Seq

    R 306 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 507 77

Repositories

Showing 10 of 153 repositories
  • 8cubeDB Public

    Query gene specificity in the founder mouse strains

    pachterlab/8cubeDB’s past year of commit activity
    Python 0 BSD-2-Clause 0 0 0 Updated Oct 30, 2025
  • CJP_2025 Public
    pachterlab/CJP_2025’s past year of commit activity
    Jupyter Notebook 0 BSD-2-Clause 0 0 0 Updated Oct 30, 2025
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    pachterlab/gget’s past year of commit activity
    Python 1,066 BSD-2-Clause 78 19 1 Updated Oct 29, 2025
  • cbrc-spec Public
    pachterlab/cbrc-spec’s past year of commit activity
    HTML 0 0 0 0 Updated Oct 29, 2025
  • 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 174 BSD-2-Clause 28 0 1 Updated Oct 27, 2025
  • varseek Public
    pachterlab/varseek’s past year of commit activity
    Python 15 BSD-2-Clause 0 0 0 Updated Oct 22, 2025
  • FLP_2024 Public

    Repository for the virial theorem and Price equation paper

    pachterlab/FLP_2024’s past year of commit activity
    Jupyter Notebook 2 BSD-2-Clause 0 0 0 Updated Oct 22, 2025
  • splitcode Public

    Flexible and efficient parsing, interpreting and editing of sequencing reads

    pachterlab/splitcode’s past year of commit activity
    C 44 BSD-2-Clause 4 16 2 Updated Oct 20, 2025
  • LP_2021 Public
    pachterlab/LP_2021’s past year of commit activity
    TeX 51 BSD-2-Clause 6 1 0 Updated Oct 18, 2025
  • wompwomp Public
    pachterlab/wompwomp’s past year of commit activity
    R 22 BSD-2-Clause 0 0 0 Updated Oct 17, 2025
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