Showing : DESEQ2 • reset
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
updated 1 day ago by 42k • written 2 days ago by • 0
4
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5
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479
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
3 days ago LuciaNhu • 0
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1
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314
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Average expression of genes across replicates
DESeq2
updated 5 days ago by ★ 4.5k • written 6 days ago by • 0
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73
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
8 days ago info ▴ 10
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10
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1.1k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
9 days ago • updated 2 days ago Denise • 0
0
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1
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282
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Deseq to output continous sequencing data
DESeq2
updated 10 days ago by 42k • written 27 days ago by • 0
1
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4
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650
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Adjusted p-values become NA when sub-setting samples
DESeq2
28 days ago • updated 1 day ago txema.heredia • 0
3
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3
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734
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 12 days ago by • 0
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2
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262
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 16 days ago by • 0
0
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1
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237
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
2
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3
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937
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Analysis of large RNA-Seq Datasets
DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
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4
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679
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DESeq2 - interactions when using factors concatenated into group
DESeq2
21 days ago • updated 13 days ago boczniak767 ▴ 740
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1
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158
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
22 days ago JY • 0
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1
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239
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 22 days ago by 42k • written 23 days ago by • 0
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2
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169
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how to extract expression matrix post deseq2
DESeq2
written 22 days ago by • 0
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2
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160
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Using Normalized Counts in DESeq2
DESeq2
updated 23 days ago by 42k • written 23 days ago by • 0
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2
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200
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When running contrasts, does it use normalized read counts?
DESeq2
24 days ago Katherine • 0
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1
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166
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 25 days ago by ★ 1.4k • written 28 days ago by • 0
3
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4
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413
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
27 days ago Eva ▴ 10
1
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4
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432
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 23 days ago by ★ 4.5k • written 5 weeks ago by • 0
0
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1
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144
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
3
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11
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638
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 4 weeks ago by • 0
2
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4
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351
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
4 weeks ago jihoon.kim.1495 ▴ 10
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6
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725
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 12 days ago by 42k • written 4 weeks ago by • 0
5
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4
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394
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 4 weeks ago by ★ 4.5k • written 5 weeks ago by • 0
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2
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243
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
4 weeks ago paul.meraner • 0
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0
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158
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
4 weeks ago • updated 8 days ago info ▴ 10
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5
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469
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heatmap with batch effect
DESeq2 BatchEffect
5 weeks ago • updated 4 weeks ago tothuhien • 0
0
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2
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321
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
1
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1
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218
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
1
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1
reply
210
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 5 weeks ago by ★ 4.5k • written 5 weeks ago by • 0
1
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1
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297
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 5 weeks ago by ★ 4.5k • written 5 weeks ago by • 0
1
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2
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406
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 10
0
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2
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668
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
1
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2
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454
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 5 weeks ago by 42k • written 7 weeks ago by ▴ 10
1
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6
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647
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 20 days ago by ★ 4.5k • written 6 weeks ago by • 0
0
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1
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269
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
17
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9
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6.9k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7 weeks ago by 67k • written 8.4 years ago by ▴ 10
0
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1
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258
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
0
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2
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476
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 8 weeks ago by ★ 1.4k • written 9 weeks ago by • 0
0
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5
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1.6k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.5 years ago by • 0
3
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6
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1.4k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 8 weeks ago by 42k • written 9 weeks ago by • 0
3
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6
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27k
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Deseq: What does "BaseMean" mean?
deseq2
written 6.1 years ago by • 0
0
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2
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829
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 9 weeks ago by ★ 1.4k • written 10 weeks ago by • 0
4
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11
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738
views
Size factor normalized counts for between sample comparisons - correct?
DESeq2
10 weeks ago boczniak767 ▴ 740
3
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4
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404
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Gene filtering in DESeq2
DESeq2
updated 10 weeks ago by ★ 4.5k • written 10 weeks ago by • 0
0
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2
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394
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 10 weeks ago by • 0
1
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2
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274
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Deseq2 - differenc in results
DESeq2
written 10 weeks ago by • 0
0
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7
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585
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DESeq design with and without intercept is giving different results
DESeq2
written 10 weeks ago by • 0
1
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5
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738
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 10 weeks ago by 51k • written 11 weeks ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load by andrew.gibbons • 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Answer: Differential Expression Analysis with unbalanced batches without replication bet by Gordon Smyth 51k
> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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