Author: Michael I Love

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Preprints

Plotgardener: Cultivating precise multi-panel figures in R

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Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference

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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

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Alignment and mapping methodology influence transcript abundance estimation

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Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation

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SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data

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Flexible expressed region analysis for RNA-seq with derfinder

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A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

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zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications

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An approach for normalization and quality control for NanoString RNA expression data

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Static And Dynamic DNA Loops Form AP-1 Bound Activation Hubs During Macrophage Development

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Cell-type specific effects of genetic variation on chromatin accessibility during human neuronal differentiation

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Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

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Nonparametric expression analysis using inferential replicate counts

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Comparative analysis of neutrophil and monocyte epigenomes

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MOVIE: Multi-Omics VIsualization of Estimated contributions

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MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies

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Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications

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Genetic influences on cell type specific gene expression and splicing during neurogenesis elucidate regulatory mechanisms of brain traits

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MRLocus: identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity

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Tximeta: reference sequence checksums for provenance identification in RNA-seq

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Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

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Compression of quantification uncertainty for scRNA-seq counts

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A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

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Assessing exposure effects on gene expression

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Silhouette width using generalized mean - a flexible method for assessing clustering efficiency

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DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing

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ACTOR: a latent Dirichlet model to compare expressed isoform proportions to a reference panel

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A framework for transcriptome-wide association studies in breast cancer in diverse study populations

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Gene-level germline contributions to clinical risk of recurrence scores in Black and White breast cancer patients

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Evaluating brain structure traits as endophenotypes using polygenicity and discoverability

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Distribution-based comprehensive evaluation ofmethods for differential expression analysis inmetatranscriptomics

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