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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 682 173

  2. kb_python kb_python Public

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

    Python 161 24

  3. ffq ffq Public

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

    Python 574 48

  4. gget gget Public

    🧬 gget enables efficient querying of genomic reference databases

    Python 1k 77

  5. sleuth sleuth Public

    Differential analysis of RNA-Seq

    R 304 95

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

    Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

    Jupyter Notebook 484 77

Repositories

Showing 10 of 142 repositories
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    pachterlab/gget’s past year of commit activity
    Python 1,024 BSD-2-Clause 77 18 1 Updated May 19, 2025
  • CGCCP_2023 Public

    scVI extension for unspliced RNA

    pachterlab/CGCCP_2023’s past year of commit activity
    Jupyter Notebook 16 BSD-2-Clause 1 1 0 Updated May 18, 2025
  • LP_2021 Public
    pachterlab/LP_2021’s past year of commit activity
    TeX 46 BSD-2-Clause 8 1 0 Updated May 15, 2025
  • gget_examples Public

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

    pachterlab/gget_examples’s past year of commit activity
    Jupyter Notebook 34 BSD-2-Clause 5 0 0 Updated May 14, 2025
  • SBP_2025 Public

    Code for reproducing the results in the klue manuscript

    pachterlab/SBP_2025’s past year of commit activity
    Jupyter Notebook 2 BSD-2-Clause 0 0 0 Updated May 14, 2025
  • klue Public
    pachterlab/klue’s past year of commit activity
    HTML 4 BSD-2-Clause 0 0 0 Updated May 14, 2025
  • KP_2025 Public
    pachterlab/KP_2025’s past year of commit activity
    Jupyter Notebook 3 BSD-2-Clause 0 0 0 Updated May 13, 2025
  • FP_2025 Public
    pachterlab/FP_2025’s past year of commit activity
    Jupyter Notebook 0 BSD-2-Clause 0 0 0 Updated May 12, 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 161 BSD-2-Clause 24 2 1 Updated May 11, 2025
  • LSCHWCP_2023 Public

    Identification of viral RdRPs in single-cell RNA sequencing data

    pachterlab/LSCHWCP_2023’s past year of commit activity
    Jupyter Notebook 10 BSD-2-Clause 1 1 0 Updated May 8, 2025
View all repositories

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