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crtpower-manuscript

custom-shell-scripts

import-frangieh-2021

import-gasperini-2019-v2

Import Gasperini 2019 (version 2)

import-gasperini-2019-v3

import-nagy-2020

Downloads the Nagy 2020 dataset and converts it into ODM format.

import-papalexi-2021

Import and process data from Papalexi 2021.

import-replogle-2022

import-schraivogel-2020

jamboree-2024-inference

katlabutils

katsevich-lab.github.io

Katsevich Lab website

lab-resources

lowmoi

A unified interface for existing methods

ondisc-manuscript

Code for the `ondisc` manuscript

ondiscdata

Example data for `ondisc` package.

pc-grna-pipeline

A pipeline for carrying out the positive control gRNA analysis.

sceptre

An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.

sceptre-igvf

sceptre-manuscript

This repository contains code for the paper "Conditional resampling improves calibration and sensitivity in single cell CRISPR screen analysis" by Barry et al. 2020.

sceptre2-manuscript

Reproduction code for "Robust differential expression testing for single-cell CRISPR screens at low multiplicity-of-infection" by Barry et al. 2023

sceptre3-manuscript

Code for the sceptre3 manuscript

sceptre3-project-v2

Repo for the sceptre3 project.

sceptredata

Example data for use in the `sceptre` and `ondisc` packages

sceptrehub

`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.

simulatr

Portable and scalable simulation studies

simulatr-command-line

Development scripts for `simulatr`.

simulatr-pipeline

The simulatr Nextflow pipeline

spacrt

All functions we will use for the spacrt project.

symcrt

A collection of methods for the symcrt project