Knockoffs for analysis of GWAS summary statistics

He, Z., B. Chu, J. Yang, J. Gu, Chen, Z., L. Liu, T. Morrison, M. Belloy, X. Qi, N. Hejazi, M. Mathur, Y. LeGuenn, H. Tang, T. Hastie, I. Ionita-Iaza, C. Sabatti and E Candes (2024) Beyond guilty by association at scale: searching for causal variants on the basis of genome-wide summary statistics bioRxiv doi: https://doi.org/10.1101/2024.02.28.582621

Knockoffs in Julia

Benjamin B Chu, Jiaqi Gu, Zhaomeng Chen, Tim Morrison, Emmanuel Candes, Zihuai He, Chiara Sabatti (2023) Second-order group knockoffs with applications to GWAS arXiv:2310.15069

KnockoffZoom

M. Sesia, E. Katsevich, S. Bates, E. Candès, C. Sabatti (2020) Multi-resolution localization of causal variants across the genome Nature Communications 11: 1-10

AEGIS

J. Zhu, Q. Zhao, E. Katsevich, C. Sabatti (2018) Exploratory Gene Ontology Analysis with Interactive Visualization

GeneSLOPE

Brzyski, D., C. Peterson, E. Candes, M. Bogdan, C. Sabatti, P. Sobczyk (2016) "Controlling the Rate of GWAS False Discoveries"

TreeQTL

Peterson, C., M. Bogomolov, Y. Benjamini, C. Sabatti (2015) "Hierarchical error control for eQTL studies"

ptyco

Stell, L. and C. Sabatti (2015) "Genetic variant selection: learning across traits and sites," arXiv:1504.00946

Piet

Z. Zhang, K. Lange, C. Sabatti (2012) Reconstructing DNA copy number by joint segmentation of multiple sequences

Bayesian sparse hidden components analysis

C. Sabatti and G. James "Bayesian sparse hidden components analysis for transcription regulation networks" Bioinformatics, Advance Access published on December 20, 2005

Text file containing an R function that samples from the posterior distribution of A,P,Z: BNCA.R

Note that to perform the transcription network reconstruction described in the article, you need to have a prior probability on Z, derived from sequence analysis. In Sabatti and James (2005) we use the Vocabulon algorithm with this goal.

The R Project for Statistical Computing

Vocabulon

Sabatti, C. and K. Lange (2002) "Genomewide motif identification using a dictionary model," IEEE Proceedings 90: 1803-1810.

Sabatti, C., L. Rohlin, K. Lange, and J. C. Liao (2005) "Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites" Bioinformatics, 21: 922 - 931.

Vocabulon web-site

Volume Measures

Chen, Y., C. Lin, C. Sabatti (2006) "Volume Measures for Linkage Disequilibrium," BMC Genetics 7:54.

Dowload C routines