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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

  1. kallisto kallisto Public

    Near-optimal RNA-Seq quantification

    C 625 169

  2. kb_python kb_python Public

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

    Python 141 22

  3. ffq ffq Public

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

    Python 529 45

  4. gget gget Public

    🧬 gget enables efficient querying of genomic reference databases

    Python 869 67

  5. sleuth sleuth Public

    Differential analysis of RNA-Seq

    R 300 96

  6. poseidon poseidon Public

    poseidon system - open source syringe pumps and microscope for laboratories

    Jupyter Notebook 169 52

Repositories

Showing 10 of 126 repositories
  • monod_examples Public

    Tutorials for the Monod package, which fits CME models to sequencing data.

    Jupyter Notebook 6 BSD-2-Clause 1 2 0 Updated Jun 1, 2024
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    Python 869 BSD-2-Clause 67 12 1 Updated Jun 1, 2024
  • monod Public

    The Monod package fits CME models to sequencing data.

    Python 24 BSD-2-Clause 3 3 0 Updated May 31, 2024
  • SpatialFeatureExperiment Public

    Extension of SpatialExperiment with sf

    R 32 Artistic-2.0 7 18 0 Updated May 31, 2024
  • RMEJLBASBMP_2024 Public

    Repository for the paper "The impact of package selection and versioning on single-cell RNA-seq analysis"

    Jupyter Notebook 16 BSD-2-Clause 5 0 0 Updated May 30, 2024
  • CGP_2023 Public

    Repository for meK-Means Inference Method

    Jupyter Notebook 1 BSD-2-Clause 0 0 0 Updated May 29, 2024
  • splitcode Public

    Flexible and efficient parsing, interpreting and editing of sequencing reads

    C 18 BSD-2-Clause 0 2 0 Updated May 28, 2024
  • seqspec Public

    machine-readable file format for genomic library sequence and structure

    Python 102 MIT 17 3 0 Updated May 28, 2024
  • CGCCP_2023 Public

    scVI extension for unspliced RNA

    Jupyter Notebook 10 BSD-2-Clause 0 0 0 Updated May 27, 2024
  • voyager Public

    From geospatial to spatial -omics

    R 60 Artistic-2.0 5 13 0 Updated May 18, 2024
View all repositories

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