Cover Image

Nullstrap-DE: A General Framework for Calibrating FDR and Preserving Power in DE Methods, with Applications to DESeq2 and edgeR

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Jiang, Chenxin, Wang, Changhu, Li, Jingyi Jessica
Format:	Preprint
Published:	2025
Subjects:	Methodology Genomics Applications
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Tool Choice Matters: Evaluating edgeR vs. DESeq2 for Sensitivity, Robustness, and Cross-Study Performance
by: Rezapour, Mostafa
Published: (2026)

Nullstrap: A Simple, High-Power, and Fast Framework for FDR Control in Variable Selection for Diverse High-Dimensional Models
by: Wang, Changhu, et al.
Published: (2025)

Robust Genomic Prediction and Heritability Estimation using Density Power Divergence
by: Chowdhury, Upama Paul, et al.
Published: (2024)

Causal Discovery on Dependent Mixed Data with Applications to Gene Regulatory Network Inference
by: Chen, Alex, et al.
Published: (2026)

Controlling the joint local false discovery rate is more powerful than meta-analysis methods in joint analysis of summary statistics from multiple genome-wide association studies
by: Jiang, Wei, et al.
Published: (2016)

Estimating Reproducibility in Genome-Wide Association Studies
by: Jiang, Wei, et al.
Published: (2015)

CoMMiT: Co-informed inference of microbiome-metabolome interactions via transfer learning
by: Li, Leiyue, et al.
Published: (2025)

Second-order group knockoffs with applications to GWAS
by: Chu, Benjamin B, et al.
Published: (2023)

Controlled Variable Selection from Summary Statistics Only? A Solution via GhostKnockoffs and Penalized Regression
by: Chen, Zhaomeng, et al.
Published: (2024)

A Statistical Framework for Co-Mediators of Zero-Inflated Single-Cell RNA-Seq Data
by: Ahn, Seungjun, et al.
Published: (2025)

Spatial Transcriptomics Iterative Hierarchical Clustering (stIHC): A Novel Method for Identifying Spatial Gene Co-Expression Modules
by: Higgins, Catherine, et al.
Published: (2025)

Bayesian Cox model with graph-structured variable selection priors for multi-omics biomarker identification
by: Hermansen, Tobias Østmo, et al.
Published: (2025)

Assumption-Lean Post-Integrated Inference with Surrogate Control Outcomes
by: Du, Jin-Hong, et al.
Published: (2024)

Combining Bayesian and Frequentist Inference for Laboratory-Specific Performance Guarantees in Copy Number Variation Detection
by: Talbot, Austin, et al.
Published: (2026)

High-dimensional Many-to-many-to-many Mediation Analysis
by: Nguyen, Tien Dat, et al.
Published: (2026)

Tutorial on survival modeling with applications to omics data
by: Zhao, Zhi, et al.
Published: (2023)

MitoFREQ: A Novel Approach for Mitogenome Frequency Estimation from Top-level Haplogroups and Single Nucleotide Variants
by: Andersen, Mikkel Meyer, et al.
Published: (2026)

Effect Size-Driven Pathway Meta-Analysis for Gene Expression Data
by: Villatoro-García, Juan Antonio, et al.
Published: (2025)

Shotgun DNA sequencing for human identification: Dynamic SNP selection and likelihood ratio calculations accounting for errors
by: Andersen, Mikkel Meyer, et al.
Published: (2024)

BioKlustering: a web app for semi-supervised learning of maximally imbalanced genomic data
by: Ozminkowski, Samuel, et al.
Published: (2022)

Optimizing Sample Size for Supervised Machine Learning with Bulk Transcriptomic Sequencing: A Learning Curve Approach
by: Qi, Yunhui, et al.
Published: (2024)

Non-ignorable fuzziness in granular counts: the case of RNA-seq data
by: Calcagnì, Antonio, et al.
Published: (2026)

FDR controlling procedures with dimension reduction and their application to GWAS with linkage disequilibrium score
by: Jung, Dayeon, et al.
Published: (2025)

Distribution-free screening of spatially variable genes in spatial transcriptomics
by: Wang, Changhu, et al.
Published: (2026)

Discovering Candidate Genes Regulated by GWAS Signals in Cis and Trans
by: Pal, Samhita, et al.
Published: (2024)

Benchmarking Heritability Estimation Strategies Across 86 Configurations and Their Downstream Effect on Polygenic Risk Score Performance
by: Muneeb, Muhammad, et al.
Published: (2026)

A frequentist test of proportional colocalization after selecting relevant genetic variants
by: Patel, Ashish, et al.
Published: (2024)

A robust, scalable K-statistic for quantifying immune cell clustering in spatial proteomics data
by: Wrobel, Julia, et al.
Published: (2024)

Selecting ChIP-seq Normalization Methods from the Perspective of their Technical Conditions
by: Colando, Sara, et al.
Published: (2025)

Incorporating LLM Embeddings for Variation Across the Human Genome
by: Niu, Hongqian, et al.
Published: (2025)

Unlocking the Power of Multi-institutional Data: Integrating and Harmonizing Genomic Data Across Institutions
by: Chen, Yuan, et al.
Published: (2024)

Uncovering smooth structures in single-cell data with PCS-guided neighbor embeddings
by: Ma, Rong, et al.
Published: (2025)

Longitudinal prediction of DNA methylation to forecast epigenetic outcomes
by: Leroy, Arthur, et al.
Published: (2023)

TransST: Transfer Learning Embedded Spatial Factor Modeling of Spatial Transcriptomics Data
by: Liu, Shuo Shuo, et al.
Published: (2025)

HR-VILAGE-3K3M: A Human Respiratory Viral Immunization Longitudinal Gene Expression Dataset for Systems Immunity
by: Sun, Xuejun, et al.
Published: (2025)

Controlling FDR in selecting group-level simultaneous signals from multiple data sources with application to the National Covid Collaborative Cohort data
by: Wang, Runqiu, et al.
Published: (2023)

Toward the Identifiability of Comparative Deep Generative Models
by: Lopez, Romain, et al.
Published: (2024)

BaGGLS: A Bayesian Shrinkage Framework for Interpretable Modeling of Interactions in High-Dimensional Biological Data
by: Lemanczyk, Marta S., et al.
Published: (2025)

Detecting and Correcting Sample-by-Sample Scale Distortion in RNA Sequencing Data
by: Thron, Christopher, et al.
Published: (2026)

Scalable Amortized GPLVMs for Single Cell Transcriptomics Data
by: Zhao, Sarah, et al.
Published: (2024)