Pinned Repositories
sceptre
An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.
adaptiveperm
Adaptive permutation testing based on anytime-valid inference and betting
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
glmeiv
A GLM-based variant of the errors-in-variables model.
ondisc
Space- and time-optimal algorithms for large single-cell expression matrices, with a focus on single-cell CRISPR screens.
sceptre-pipeline-1
The sceptre Nextflow pipeline.
simulatr
Portable and scalable simulation studies
timothy-barry.github.io
My website
timothy-barry's Repositories
timothy-barry/ondisc
Space- and time-optimal algorithms for large single-cell expression matrices, with a focus on single-cell CRISPR screens.
timothy-barry/glmeiv
A GLM-based variant of the errors-in-variables model.
timothy-barry/adaptiveperm
Adaptive permutation testing based on anytime-valid inference and betting
timothy-barry/sceptre-pipeline-1
The sceptre Nextflow pipeline.
timothy-barry/simulatr
Portable and scalable simulation studies
timothy-barry/timothy-barry.github.io
My website
timothy-barry/camp
Permutation testing with powerful statistics
timothy-barry/CRISPR-JAMBOREE
2nd IGVF CRISPR-JAMBOREE
timothy-barry/glmeiv-manuscript
Code for reproducing analyses reported in "Exponential family measurement error models for single-cell CRISPR screens" (2022).
timothy-barry/glmeiv-pipeline
A Nextflow-based pipeline for GLM-EIV.
timothy-barry/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.
timothy-barry/fas_cluster_setup
timothy-barry/glmeiv-project
Scripts for the glmeiv manuscript
timothy-barry/import-frangieh-2021
timothy-barry/import-gasperini-2019
Download and process the Gasperini 2019 data
timothy-barry/import-xie-2019
Code to import Xie 2019 data.
timothy-barry/katlabutils
timothy-barry/nf_docker_demo
A demo Nextflow script using a simple Docker image.
timothy-barry/nf_docker_odm
Example Nextflow pipeline using ondisc.
timothy-barry/ondiscdata
Example data for the ondisc examples and vignettes.
timothy-barry/permtools
Tools for permutation testing
timothy-barry/proposal
Items related to my proposal
timothy-barry/sceptre-book
timothy-barry/sceptre-pipeline2
The second version of the sceptre Nextflow pipeline.
timothy-barry/sceptre2
The sceptre2 package.
timothy-barry/sceptreData
Example datasets for use in the `sceptre` vignettes
timothy-barry/schmidt-2022-analysis
timothy-barry/sequential_perm_testing
Code for multiple sequential permutation testing paper
timothy-barry/simulatr-command-line
Development scripts for `simulatr`.
timothy-barry/simulatr-pipeline
The simulatr Nextflow pipeline