Showing : differential gene expression • reset
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Why DESeq2 and edgeR give different results?
deseq2 rnaseq differential gene expression edger
updated 4.3 years ago by 53k • written 7.4 years ago by ▴ 120
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4
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edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
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Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 120
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3
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TPM data Differential expression analysis
edger limma differential gene expression
updated 3.4 years ago by 53k • written 7.4 years ago by • 0
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3
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898
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Differentially expressed genes detection between three classes with a batch effect in DESeq2
deseq2 batch effect differential gene expression
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
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1
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Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 7.4 years ago by ★ 29k • written 7.4 years ago by • 0
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Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 7.4 years ago by ▴ 280 • written 7.4 years ago by ▴ 40
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Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
edger differential gene expression upregulated genes downregulated genes
updated 7.5 years ago by • 0 • written 7.5 years ago by ▴ 60
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Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
7.5 years ago David R ▴ 90
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DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
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2
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3.9k
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Going crazy with normalizing TCGA raw rsem gene count
cancer tcga normalization rnaseq differential gene expression
updated 7.5 years ago by • 0 • written 10.4 years ago by • 0
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Job: PhD Studentship - Investigating Regulation of Transcription and Translation in Prostate Cancer
mirna riboseq smallrna differential gene expression Job
7.5 years ago Andy Lynch ▴ 120
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Upregulation and Downregulation of Gene Ontology terms
microarray david differential gene expression GO
7.5 years ago seendey16 • 0
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1
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1.5k
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Differential Coexpression Analysis
differential analysis differential gene expression coexpression correlation
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 20
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3
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edgeR multifactorial analysis implementation with RNA-Seq data
edger multifactorial design multiple comparisons differential gene expression
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 840
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0
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650
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plotMA is not centered around zero for logFC
microarray differential gene expression
7.6 years ago twentestat • 0
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3
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1.7k
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Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
7.6 years ago cherlyn.t • 0
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8
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Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
7.6 years ago Marina ▴ 40
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1.2k
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Requesting help with RNA-Seq differential gene analysis
differential gene expression gene expression clustering gene regulatory network normalization
7.6 years ago sagnik • 0
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2
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DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2 goseq rnaseq go enrichment differential gene expression
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
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Performing differential gene analysis on RT PCR experimental data
differential gene expression
updated 7.6 years ago by 53k • written 7.7 years ago by ▴ 10
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967
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Pairwise Comparison between A Large Number of Groups
deseq2 differential gene expression
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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3.7k
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DESeq2 design model/contrasts question 3 level condition
deseq2 model design differential gene expression experimental design
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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2
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Differential expression of RNA seq data at gene level (for Beginner)
deseq2 differential gene expression bioconductor
updated 7.8 years ago by ▴ 130 • written 7.8 years ago by • 0
2
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3
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2.0k
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Can DESeq2/edgeR perform differential analysis for rRNA?
deseq2 edger rRNA differential gene expression
7.8 years ago r.aprianto ▴ 30
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RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 10
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What package should I use to retrieve chromosome location for Affymetrix id of gene symbol id while doing gene expression microarray analysis ?
affymetrix microarrays differential gene expression
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 20
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Applying replaceOutliers rather than throwing out genes when model includes continuous variable
deseq2 rnaseq differential gene expression differential expression
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
2
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Loads, really loads of DEGs after edgeR differential analysis
rnaseq edger normalization differential gene expression
7.8 years ago David R ▴ 90
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3.0k
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Constant High Padj Values
deseq2 differential gene expression multiple factor design padj
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
2
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9
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SNP-level Allele-specific expression detection using DESeq2 in an unpaired experimental design
deseq2 rnaseq differential gene expression
7.9 years ago • updated 7.8 years ago engelbrecht.stephan ▴ 10
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Differential expression between multiple groups
multiple groups differential gene expression microarray
7.9 years ago A ▴ 60
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5.4k
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deseq2 analysis with multiple factors and interaction terms
deseq2 multiple factor design differential analysis differential gene expression
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
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4
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1.7k
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limma. After running a differential expression analysis... Can you get the individual gene expression levels between individual contrasts for each of…
limma gene expression differential gene expression
7.9 years ago arfranco ▴ 130
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4
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Multiple differential expression analyses with DESeq2
deseq2 differential gene expression
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
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Strange distribution of logFC
edger deseq2 rnaseq differential gene expression
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 20
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Ballgown with replicates and the adjustvars option
ballgown rnaseq differential gene expression
updated 7.9 years ago by ▴ 210 • written 8.1 years ago by • 0
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Design model for DESeq2 analysis
deseq2 differential gene expression
updated 7.9 years ago by ▴ 690 • written 7.9 years ago by ▴ 20
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1.6k
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Adding gene names which are differentially expressed in the plot
edgeR plot differential gene expression
7.9 years ago fawazfebin ▴ 60
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2.2k
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Differential Expression analysis between distinct scRNA-seq datasets
scrna scrnaseq differential gene expression
updated 7.9 years ago by ▴ 980 • written 7.9 years ago by • 0
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3
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replicates and groups of samples: what's the right DESeq2 model?
deseq2 rnaseq differential gene expression
updated 8.0 years ago by ▴ 690 • written 8.0 years ago by • 0
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comparison of expression between orthologous species
rnaseq differential gene expression
8.0 years ago laksharikrish • 0
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5
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Differential gene expression: common changes in response to treatment across cell types
deseq2 differential gene expression
updated 8.0 years ago by ▴ 690 • written 8.0 years ago by ▴ 10
3
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6
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Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix toptable makecontrasts differential gene expression
8.0 years ago stinehedensted • 0
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3
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1.8k
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Differential expression of individual genes using edgeR
edger differential gene expression
8.0 years ago fawazfebin ▴ 60
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Differential gene expression for multi-factorial experiment using edgeR
edger differential gene expression multiple factor design
updated 8.0 years ago by ★ 29k • written 8.0 years ago by • 0
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5
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3.8k
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Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
8.0 years ago lirongrossmann ▴ 80
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Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 8.0 years ago by ▴ 690 • written 8.0 years ago by ▴ 50
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Differential expression of nomalised and log2 transformed data in limma
limma lmfit model.matrix differential gene expression
8.0 years ago stinehedensted • 0
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2.0k
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DESeq2 biological replicates and RIN values
deseq2 differential gene expression covariates rnaseq
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
272 results • Page 2 of 6
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Answer: Help with defining groups by Gordon Smyth 53k
Defining sample groups is separate to reading in the DIA-NN data, because the sample conditions and covariates are not necessarily coded in…
Comment: Sharing a collection of datasets in ExperimentHub by Peter Hickey ▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi by ReinholdGaylord99 • 0
Thank you so much! https://www.nature.com/articles/s41467-021-25960-2/ [geometry dash lite](https://geometrydashlite.online)
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
I'm not sure that I understand. You have a dataset that, even after pseudo-bulking, still has 6000 samples? That is surprising. Retaining …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Hello again @gordonsmyth, I've now applied the analysis using a more detailed annotation of cell types/clusters, which includes about 100 …
Votes
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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