KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
All data used in this study	Zenodo	DOI: https://doi.org/10.5281/zenodo.6573413
DREAM5 E. coli data	Sage Bionetworks	https://dreamchallenges.org/dream-5-network-inference-challenge/
Mouse transcription factors	AnimalTFDB	https://guolab.wchscu.cn/AnimalTFDB#!/
Human transcription factors	Lambert et al.102	http://humantfs2.ccbr.utoronto.ca/download.php
SHARE-seq data	Ma et al.70	GEO: GSM4156608 and GEO: GSM4156597
10X multiomics data	10x Genomics website	https://www.10xgenomics.com/datasets/pbmc-from-a-healthy-donor-no-cell-sorting-10-k-1-standard-2-0-0
Human and mouse transcription factor targets	ChIP-atlas	http://dbarchive.biosciencedbc.jp/kyushu-u/metadata/experimentList.tab
E. coli high-throughput gold standards	RegulonDB v10.9	https://regulondb.ccg.unam.mx/ht
E. coli curated gold standards	RegulonDB v10.9	https://regulondb.ccg.unam.mx/releasesNote/date=2021-04-02&version=10.9
Software and algorithms
Modification of the BoolODE framework	This paper	DOI: https://doi.org/10.5281/zenodo.10063178
Modification of the BEELINE framework	This paper	DOI: https://doi.org/10.5281/zenodo.10063174
E. coli analysis	This paper	DOI: https://doi.org/10.5281/zenodo.10063164
Multi-omics analysis	This paper	DOI: https://doi.org/10.5281/zenodo.10688721
Demonstration of knockoff construction speedups and calibration on incomplete gold standards	This paper	DOI: https://doi.org/10.5281/zenodo.10063183
Faster implementation of the Gaussian mirror (R package)	This paper	DOI: https://doi.org/10.5281/zenodo.10063192
Faster implementation of knockoff construction (limited Julia interface)	This paper	DOI: https://doi.org/10.5281/zenodo.10063198
Faster implementation of knockoff construction (limited Python interface)	This paper	DOI: https://doi.org/10.5281/zenodo.10063196
Faster implementation of knockoff construction (R package)	This paper	DOI: https://doi.org/10.5281/zenodo.10063187