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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 622 169

  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 864 64

  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 167 52

Repositories

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