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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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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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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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Differential gene expression (DGE) analysis in persons with a history of giardiasis
Giardiasis, which is caused by Giardia duodenalis , has clinical symptoms such as steatorrhea and can be very dangerous in children . In addition, some...
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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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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...
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Differential gene expression analysis reveals the fast-growth mechanisms in Melia dubia at different stand ages
BackgroundMelia dubia Cav. is a fast-growing multipurpose tree suitable for agroforestry and has been widely cultivated for wood-based industries,...
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Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs
By profiling gene expression in individual cells, single-cell RNA-sequencing (scRNA-seq) can resolve cellular heterogeneity and cell-type gene...
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Epigenetic Control of Gene Expression
Genetic mutations lead to inheritable changes in the traits. Alterations in genetic features may also be caused by chromatin modifications without...
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Gene Co-expression Network Analysis
Gene co-expression analysis is a data analysis technique that helps identify groups of genes with similar expression patterns across several...
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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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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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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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Clearing of Vascular Tissue in Arabidopsis thaliana for Reporter Analysis of Gene Expression
To study the gene regulatory mechanisms modulating development is essential to visualize gene expression patterns at cellular resolution. However,...
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Meta-analysis of Gene Activity (MAGA) Contributions and Correlation with Gene Expression, Through GAGAM
It is well-known how sequencing technologies propelled cellular biology research in the latest years, giving an incredible insight into the basic...
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Callose Metabolism in Flax Fibers During Gravity Response: Analysis of Gene Expression
AbstractMotor responses of plants related to tropisms are usually carried out using elongation growth mechanisms. However, this study examined...
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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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Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment
BackgroundRNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the...
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Identification of eQTLs and differential gene expression associated with fetal programming in beef cattle
This study assessed differential gene expression and identified expression quantitative trait loci (eQTLs) from samples of Longissimus lumborum ...
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Gene Expression in Medicinal Plants in Stress Conditions
Medicinal plants have been in use for hundreds of years for the betterment of mankind against a plethora of ailments in different parts of the world....