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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 645 170

  2. kb_python kb_python Public

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

    Python 142 23

  3. ffq ffq Public

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

    Python 538 47

  4. gget gget Public

    🧬 gget enables efficient querying of genomic reference databases

    Python 911 73

  5. sleuth sleuth Public

    Differential analysis of RNA-Seq

    R 303 94

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

    Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

    Jupyter Notebook 389 61

Repositories

Showing 10 of 129 repositories
  • 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 142 BSD-2-Clause 23 1 1 Updated Aug 14, 2024
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    pachterlab/gget’s past year of commit activity
    Python 911 BSD-2-Clause 73 17 2 Updated Aug 14, 2024
  • FGP_2024 Public
    pachterlab/FGP_2024’s past year of commit activity
    Jupyter Notebook 3 0 1 0 Updated Aug 14, 2024
  • monod Public

    The Monod package fits CME models to sequencing data.

    pachterlab/monod’s past year of commit activity
    Python 27 BSD-2-Clause 3 3 0 Updated Aug 14, 2024
  • splitcode Public

    Flexible and efficient parsing, interpreting and editing of sequencing reads

    pachterlab/splitcode’s past year of commit activity
    C 38 BSD-2-Clause 0 10 0 Updated Aug 14, 2024
  • ffq Public

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

    pachterlab/ffq’s past year of commit activity
    Python 538 MIT 47 2 3 Updated Aug 13, 2024
  • HSSHMP_2024 Public

    Code for reproducing the results in the second version of the preprint "Accurate quantification of single-nucleus and single-cell RNA-seq transcripts"

    pachterlab/HSSHMP_2024’s past year of commit activity
    Jupyter Notebook 3 BSD-2-Clause 1 0 0 Updated Aug 12, 2024
  • seqspec Public

    machine-readable file format for genomic library sequence and structure

    pachterlab/seqspec’s past year of commit activity
    Python 107 MIT 17 5 0 Updated Aug 9, 2024
  • LSCHWCP_2023 Public

    Identification of viral RNA in single-cell RNA sequencing data

    pachterlab/LSCHWCP_2023’s past year of commit activity
    Jupyter Notebook 1 BSD-2-Clause 1 1 0 Updated Aug 9, 2024
  • SpatialFeatureExperiment Public

    Extension of SpatialExperiment with sf

    pachterlab/SpatialFeatureExperiment’s past year of commit activity
    R 36 Artistic-2.0 7 17 0 Updated Aug 7, 2024
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