timothy-barry

ondisc

Space- and time-optimal algorithms for large single-cell expression matrices, with a focus on single-cell CRISPR screens.

glmeiv

A GLM-based variant of the errors-in-variables model.

sceptre-pipeline

This is the repository for the sceptre Nextflow pipeline. The pipeline combines sceptre, ondisc, and Nextflow to enable massively scalable and statistically sound single-cell CRISPR screen analysis.

sceptre-pipeline-1

The sceptre Nextflow pipeline.

simulatr

Portable and scalable simulation studies

timothy-barry.github.io

My website

camp

Permutation testing with powerful statistics

Collections-in-R

Code used to generate the data and figures in the manuscript "Collections in R: Review and Proposal."

CRISPR-JAMBOREE

2nd IGVF CRISPR-JAMBOREE

crisprdata

A data package storing some example scCRISPR screen data.

glmeiv-manuscript

Code for reproducing analyses reported in "Exponential family measurement error models for single-cell CRISPR screens" (2022).

glmeiv-pipeline

A Nextflow-based pipeline for GLM-EIV.

glmeiv-project

Scripts for the glmeiv manuscript

import-frangieh-2021

import-gasperini-2019

Download and process the Gasperini 2019 data

import-xie-2019

Code to import Xie 2019 data.

katlabutils

nf_docker_demo

A demo Nextflow script using a simple Docker image.

nf_docker_odm

Example Nextflow pipeline using ondisc.

ondiscdata

Example data for the ondisc examples and vignettes.

proposal

Items related to my proposal

readr

Read flat files (csv, tsv, fwf) into R

sceptre-book

sceptre-pipeline2

The second version of the sceptre Nextflow pipeline.

sceptre2

The sceptre2 package.

sceptreData

Example datasets for use in the `sceptre` vignettes

schmidt-2022-analysis

simulatr-command-line

Development scripts for `simulatr`.

simulatr-pipeline

The simulatr Nextflow pipeline