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Nonparametric analysis of contributions to variance in genomics and epigenomics data

https://doi.org/10.1101/314112
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/0377-0427(87)90125-7openalex-snapshot
Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
inferredcites →https://doi.org/10.1038/nature08514openalex-snapshot
Human DNA methylomes at base resolution show widespread epigenomic differences
inferredcites →https://doi.org/10.1038/nbt.1630openalex-snapshot
GREAT improves functional interpretation of cis-regulatory regions
inferredcites →https://doi.org/10.1038/nbt.2931openalex-snapshot
Normalization of RNA-seq data using factor analysis of control genes or samples
inferredcites →https://doi.org/10.1038/nbt.3000openalex-snapshot
Detecting and correcting systematic variation in large-scale RNA sequencing data
inferredcites →https://doi.org/10.1038/ng.2653openalex-snapshot
The Genotype-Tissue Expression (GTEx) project
inferredcites →https://doi.org/10.1038/nmeth.2688openalex-snapshot
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
inferredcites →https://doi.org/10.1038/nprot.2011.457openalex-snapshot
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
inferredcites →https://doi.org/10.1038/nrg2825openalex-snapshot
Tackling the widespread and critical impact of batch effects in high-throughput data
inferredcites →https://doi.org/10.1073/pnas.1400517111openalex-snapshot
Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity
inferredcites →https://doi.org/10.1073/pnas.1413624111openalex-snapshot
Comparison of the transcriptional landscapes between human and mouse tissues
inferredcites →https://doi.org/10.1093/bioinformatics/bts034openalex-snapshot
The sva package for removing batch effects and other unwanted variation in high-throughput experiments
inferredcites →https://doi.org/10.1093/biostatistics/kxr034openalex-snapshot
Using control genes to correct for unwanted variation in microarray data
inferredcites →https://doi.org/10.1093/nar/gku864openalex-snapshot
svaseq: removing batch effects and other unwanted noise from sequencing data
inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot
limma powers differential expression analyses for RNA-sequencing and microarray studies
inferredcites →https://doi.org/10.1126/science.1105136openalex-snapshot
The ENCODE (ENCyclopedia Of DNA Elements) Project
inferredcites →https://doi.org/10.1126/science.1141319openalex-snapshot
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
inferredcites →https://doi.org/10.1126/sciimmunol.aag0192openalex-snapshot
Epigenomics of human CD8 T cell differentiation and aging
inferredcites →https://doi.org/10.1186/1471-2164-9-285openalex-snapshot
Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
inferredcites →https://doi.org/10.1186/gb-2010-11-10-r106openalex-snapshot
Differential expression analysis for sequence count data
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.12688/f1000research.6536.1openalex-snapshot
A reanalysis of mouse ENCODE comparative gene expression data
inferredcites →https://doi.org/10.48550/arxiv.1407.4443openalex-snapshot
On the Complexity of Best Arm Identification in Multi-Armed Bandit Models
inferredcites →https://doi.org/10.48550/arxiv.1512.01286openalex-snapshot
Adjusting for Chance Clustering Comparison Measures

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.cell.2021.05.002openalex-snapshot
A global metagenomic map of urban microbiomes and antimicrobial resistance
inferred← citeshttps://doi.org/10.1038/s42003-022-03975-9openalex-snapshot
A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses
inferred← citeshttps://doi.org/10.1101/724526openalex-snapshot
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
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