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Differential Gene Expression During Somatic Embryogenesis
Somatic embryogenesis is a complex developmental program in which somatic cells are induced for a commitment towards forming totipotent...
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Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation
BackgroundChanging cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood...
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eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings
BackgroundSingle-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of...
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N-of-one differential gene expression without control samples using a deep generative model
Differential analysis of bulk RNA-seq data often suffers from lack of good controls. Here, we present a generative model that replaces controls,...
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Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the...
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Differential Expression of MicroRNAs in the Kidneys of Rats Following Sustained Swimming Exercise
AbstractSwimming exercise is reported to have protective effects on kidney function. Previous studies have indicated that microRNAs (miRNAs) are...
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Differential Expression Feature Extraction (DEFE): A Case Study in Wheat FHB RNA-Seq Data Analysis
In differential gene expression data analysis, one objective is to identify groups of co-expressed genes from a large dataset in order to detect the...
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GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership
Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell...
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transcAnalysis: A Snakemake Pipeline for Differential Expression and Post-transcriptional Modification Analysis
The transcAnalysis pipeline is a comprehensive tool that allows the analysis of transcriptome data. The pipeline allows for analysis of differential...
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PRANA: an R package for differential co-expression network analysis with the presence of additional covariates
BackgroundAdvances in sequencing technology and cost reduction have enabled an emergence of various statistical methods used in RNA-sequencing data,...
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Iterative Clustering for Differential Gene Expression Analysis
The Next Generation Sequencing technologies provide large volumes of DNA-seq and RNA-seq data. A central part of their investigation is the task for...
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Cell type-specific inference of differential expression in spatial transcriptomics
A central problem in spatial transcriptomics is detecting differentially expressed (DE) genes within cell types across tissue context. Challenges to...
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Mesenchymal stem cells (MSCs) from the mouse bone marrow show differential expression of interferon regulatory factors IRF-1 and IRF-2
BackgroundInterferon regulatory factors (IRF-1 and IRF-2) are transcription factors widely implicated in various cellular processes, including...
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FastCAR: fast correction for ambient RNA to facilitate differential gene expression analysis in single-cell RNA-sequencing datasets
Cell type-specific differential gene expression analyses based on single-cell transcriptome datasets are sensitive to the presence of cell-free mRNA...
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Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing
BackgroundA gap currently exists between genetic variants and the underlying cell and tissue biology of a trait, and expression quantitative trait...
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LENG8-AS1: A Prognostic Biomarker in Colorectal Cancer-Differential Expression and Clinical Implications
Colorectal cancer (CRC) manifests as a prevalent malignancy marked by distinct gene expression patterns. In the intricate landscape of cancer...
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Uncertainty-Aware Protein-Level Quantification and Differential Expression Analysis of Proteomics Data with seaMass
seaMass is an R package for protein-level quantification, normalization, and differential expression analysis of proteomics mass spectrometry data...
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Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages
BackgroundHexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity...
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msmsEDA & msmsTests: Label-Free Differential Expression by Spectral Counts
msmsTests is an R/Bioconductor package providing functions for statistical tests in label-free LC-MS/MS data by spectral counts. These functions aim...
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De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the...
