Pinned repositories

  1. kallisto

    Near-optimal RNA-Seq quantification

    C 255 87

  2. sleuth

    Differential analysis of RNA-Seq

    R 139 56

  • Near-optimal RNA-Seq quantification

    C 255 87 BSD-2-Clause Updated Aug 14, 2018
  • Python 4 2 GPL-3.0 Updated Aug 14, 2018
  • Some sleuth walkthroughs to help you get started

    HTML 5 3 CC-BY-4.0 Updated Jul 26, 2018
  • Python 9 Updated Jul 14, 2018
  • Differential analysis of RNA-Seq

    R 139 56 GPL-3.0 Updated Jun 28, 2018
  • Jupyter Notebook 6 2 Updated Jun 26, 2018
  • HTML Updated May 30, 2018
  • Preprocessing of single-cell RNA-Seq data for input to kallisto

    Jupyter Notebook 50 24 GPL-3.0 Updated May 1, 2018
  • Identify cell barcodes from single-cell genomics sequencing experiments

    Jupyter Notebook 24 8 MIT Updated Apr 17, 2018
  • Code to reproduce analyses from the sleuth paper

    R 12 4 Updated Apr 13, 2018
  • Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachter

    R 12 1 GPL-3.0 Updated Feb 20, 2018
  • Computing genome assembly likelihoods

    Updated Jun 23, 2017
  • Identification and correction of systematic error in high-throughput sequence data

    Perl 1 GPL-2.0 Updated Jun 23, 2017
  • Streaming fragment assignment for real-time analysis of sequencing experiments

    1 Updated Jun 22, 2017
  • Reproduce PROBer paper analysis

    Python 1 3 GPL-3.0 Updated Jun 7, 2017
  • Keep Me Around: Intron Retention Detection

    HTML 9 7 GPL-2.0 Updated May 26, 2017
  • home of the bear's lair

    CSS 9 GPL-3.0 Updated May 19, 2017
  • Examples of kallisto + sleuth

    Python 10 5 GPL-3.0 Updated May 18, 2017
  • PROBer: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays

    C++ 2 2 Updated Mar 15, 2017
  • sleuth workflow for processing zika RNA-seq dataset

    R 4 GPL-3.0 Updated Feb 13, 2017
  • Using kallisto for metagenomic analysis

    Python 39 7 Updated Jan 12, 2017
  • materials and website for the 2016 kallisto sleuth workshop

    CSS 9 3 Updated Nov 7, 2016
  • Analysis from kallisto paper

    HTML 22 8 Updated Feb 10, 2016
  • Just some useful Vagrant boxes

    Ruby Updated Aug 25, 2015
  • A set of (regression) tests for kallisto

    Updated Jun 13, 2015