Bioconductor - edgeR
Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear …
This guide provides an overview of the Bioconductor package edgeR for di erential expres-sion analyses of read counts arising from RNA-Seq, SAGE or similar technologies [40]. The package can be applied to any technology that produces read counts for genomic features.
A brief introduction to edgeR - Bioconductor
2012年10月10日 · edgeR is a package for differential analyses of read count data from sequencing technologies such as RNA-seq, ChIP-seq, ATAC-seq, BS-seq and CUT&RUN. It has particularly strong capabilities for expression analyses of RNA-seq data, including gene expression, transcript expression and tests for differential splicing.
edgeR: a Bioconductor package for differential expression …
2009年11月11日 · edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability.
Bioconductor - edgeR
Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear …
Bioconductor - edgeR
Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication. Uses empirical Bayes estimation and exact tests based on the negative binomial distribution. Also useful for differential signal analysis with …
Bioconductor Edger
Seeing 80% DE genes in timepoint groups. Why does GSEA on edgeR results for randomized samples give highly significant p-values? Why is my gene not significantly differentially expressed? What benchmark should I use for setting the EdgeR filterByExpr min.count parameter? Cross-species analysis - how to compute the mid parent value?
RNA-seq analysis of lung adenocarcinomas reveals different gene ...
We obtained RNA-seq data from paired normal and tumor tissues from 34 nonsmoking and 34 smoking patients with lung adenocarcinoma (GEO: GSE40419). R Bioconductor, edgeR, was adopted to conduct differential gene expression analysis …
Specific micro-RNA expression patterns distinguish the basal and ...
Read counts for both mRNAs and miRNAs were used as input for differential expression analysis by the R package edgeR [41, 42]. All analyses utilized a false-discovery rate (FDR) cutoff of 5%, and a fold change cutoff of 2. ... The dataset was quantile normalized and differential expression was performed using the R Bioconductor package, linear ...
GEO Accession viewer - National Center for Biotechnology Information
2024年8月1日 · Genes with fewer than 10 fragments in all samples were removed. CPM (count per million fragments) values were estimated by the R/Bioconductor package edgeR (version 3.8.6). Supplementary files format and content: The first column is Ensembl gene id. The second column is gene symbol.
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