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    37 repositories

    • spacrt

      Public
      All functions we will use for the spacrt project.
      R
      •
      Other
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • import-tian-2024

      Public
      Shell
      •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • sceptre

      Public
      An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.
      R
      •
      GNU General Public License v3.0
      •8•26•19•2•Updated Jan 18, 2025Jan 18, 2025

    • katsevich-lab.github.io

      Public
      Katsevich Lab website
      SCSS
      •1.2k•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • simulatr-pipeline

      Public
      The simulatr Nextflow pipeline
      R
      •3•0•2•0•Updated Nov 24, 2024Nov 24, 2024

    • import-peisker-2022

      Public
      R
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • lab-resources

      Public
      TeX
      •0•0•1•0•Updated Oct 19, 2024Oct 19, 2024

    • symcrt2-manuscript

      Public
      TeX
      •0•0•0•0•Updated Sep 14, 2024Sep 14, 2024

    • spacrt-manuscript

      Public
      TeX
      •0•0•0•0•Updated Aug 26, 2024Aug 26, 2024

    • katlabutils

      Public
      R
      •
      Other
      •1•0•0•0•Updated Aug 4, 2024Aug 4, 2024

    • import-morris-2023

      Public
      Code to import the Morris 2023 dataset.
      0•0•0•0•Updated Jun 28, 2024Jun 28, 2024

    • sceptrehub

      Public
      `sceptrehub` provides an interface to the example data used in the vignettes and man pages of the `sceptre` and `ondisc` packages. It also facilitates the download of `sceptre_objects` associated with real, large-scale single-cell CRISPR screen datasets.
      R
      •
      Other
      •0•0•0•0•Updated May 20, 2024May 20, 2024

    • import-replogle-2022

      Public
      R
      •0•0•1•0•Updated Apr 30, 2024Apr 30, 2024

    • sceptre3-manuscript

      Public
      Code for the sceptre3 manuscript
      R
      •0•0•0•0•Updated Apr 26, 2024Apr 26, 2024

    • sceptre3-project-v2

      Public
      Repo for the sceptre3 project.
      HTML
      •0•0•0•0•Updated Apr 26, 2024Apr 26, 2024

    • symcrt-manuscript

      Public
      TeX
      •0•1•0•0•Updated Apr 20, 2024Apr 20, 2024

    • sceptre2-manuscript

      Public
      Reproduction code for "Robust differential expression testing for single-cell CRISPR screens at low multiplicity-of-infection" by Barry et al. 2023
      R
      •
      GNU General Public License v3.0
      •0•0•14•0•Updated Apr 16, 2024Apr 16, 2024

    • lowmoi

      Public
      A unified interface for existing methods
      R
      •
      Other
      •0•1•0•0•Updated Apr 14, 2024Apr 14, 2024

    • import-gasperini-2019-v3

      Public
      R
      •0•0•0•0•Updated Apr 6, 2024Apr 6, 2024

    • sceptredata

      Public
      Example data for use in the `sceptre` and `ondisc` packages
      R
      •
      Other
      •0•0•0•0•Updated Apr 3, 2024Apr 3, 2024

    • custom-shell-scripts

      Public
      Shell
      •0•0•0•0•Updated Mar 8, 2024Mar 8, 2024

    • jamboree-2024-inference

      Public
      0•0•0•0•Updated Feb 22, 2024Feb 22, 2024

    • sceptre-igvf

      Public
      R
      •0•0•0•0•Updated Feb 12, 2024Feb 12, 2024

    • pc-grna-pipeline

      Public
      A pipeline for carrying out the positive control gRNA analysis.
      R
      •0•0•0•0•Updated Jan 19, 2024Jan 19, 2024

    • simulatr

      Public
      Portable and scalable simulation studies
      R
      •
      Other
      •3•0•1•0•Updated Dec 3, 2023Dec 3, 2023

    • import-gasperini-2019-v2

      Public
      Import Gasperini 2019 (version 2)
      R
      •0•0•0•0•Updated Jun 19, 2023Jun 19, 2023

    • crtpower-manuscript

      Public
      TeX
      •0•0•0•0•Updated Dec 19, 2022Dec 19, 2022

    • symcrt

      Public
      A collection of methods for the symcrt project
      R
      •
      Other
      •0•0•0•0•Updated Nov 20, 2022Nov 20, 2022

    • undercover-grna-pipeline

      Public
      A Nextflow pipeline to carry out the "undercover gRNA" negative control calibration assessment
      R
      •0•0•0•0•Updated Nov 15, 2022Nov 15, 2022

    • sceptre-manuscript

      Public
      This repository contains code for the paper "Conditional resampling improves calibration and sensitivity in single cell CRISPR screen analysis" by Barry et al. 2020.
      crisprsingle-cellhypothesis-testing
      TeX
      •
      MIT License
      •3•0•0•0•Updated Jul 15, 2022Jul 15, 2022