Showing : DeSeq2 • reset
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Question regarding averaging DESeq2 results.
DESeq2
3.3 years ago e.v.egeland • 0
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2
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1.3k
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DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
3.3 years ago Marie • 0
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5
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3.5k
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Issues installing DESeq2 package with R version 4.2.1
DESeq2
3.3 years ago lucabartolinimd • 0
2
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2
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2.3k
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How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
4
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5
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3.5k
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Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
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1
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831
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Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
2
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5
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1.6k
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Detection of reference genes by Deseq2
lessAbs reference_genes DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
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5
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3.2k
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DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
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3
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1.6k
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Swish: contrasts and interactions
fishpond DESeq2
updated 2.6 years ago by 43k • written 3.3 years ago by • 0
2
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2
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1.1k
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Contradictory results in smallRNA differential expression analysis using DESeq2
SmallRNA DESeq2
3.3 years ago jucosie • 0
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1
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1.4k
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Dispersion estimates with DESeq2
dispersionestimates dispersion DESeq2 estimates deseq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
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6
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2.3k
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Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
3.4 years ago • updated 3.3 years ago Weiqian ▴ 10
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1
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1.1k
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DESeq2 - Batch effect correction in 2 conditions + 2 genotypes + interaction term design
DESeq2
updated 3.3 years ago by 43k • written 3.4 years ago by • 0
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1
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1.3k
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CQN to DESeq2
cqn DESeq2
updated 3.3 years ago by 43k • written 3.4 years ago by • 0
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5
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1.5k
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what should be our references when 2 samples which I compare are treated and there is not any control?
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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1
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1.1k
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I have a query regarding differential gene expression using limma-voom.
RNASeqData DESeq2
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
2
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1
reply
1.1k
views
Subsetting a DESeq object - gene-wise dispersions
DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.4 years ago by ▴ 20
0
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1
reply
1000
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DESeq2 Interaction Term Error Occurred
interaction DESeq2
updated 3.4 years ago by ★ 1.4k • written 3.4 years ago by • 0
2
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7
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25k
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Install DESeq2
DESeq2
3.4 years ago Chris ▴ 20
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3
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1.8k
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DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics DESeq2
3.4 years ago marius.wenzel • 0
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2
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2.2k
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
3.4 years ago fluentin44 • 0
0
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1
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1.3k
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Help with featureCounts
DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
3
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2
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1.4k
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
3.4 years ago manwar • 0
0
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8
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4.5k
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DESeq2 different log2FC and p-value filtering parameters results comparison
log2 DESeq2
3.4 years ago User000 • 0
2
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4
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2.1k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 10
1
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5
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1.4k
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DeSeq2 Matched Analysis
RNASeq DESeq2
3.4 years ago Andrea • 0
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2
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2.8k
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[DESeq2] setting LFC threshold
DESeq2
3.4 years ago Shail • 0
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1
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1.9k
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lfcShrink types for Volcano plots
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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4
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1.5k
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Can I use limma::avereps to remove dupicated genes before conduct DEG based on RSEM Expected_count data?
limma RNASeq Expected_count DESeq2
3.4 years ago Yang Shi ▴ 10
0
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1
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802
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DESeq2: correct way to extract comparison of comparisons
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
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1
reply
599
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DESeq2 for CaptureSeq
CaptureSeq DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
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6
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2.0k
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Iterating over a column within colData@listData
DESeq2 iterating SummarizedExperiment
3.4 years ago BioInfoBeginnerrr • 0
1
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3
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1.6k
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LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
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7
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2.9k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
0
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9
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2.7k
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Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin DESeq2
updated 2.1 years ago by ▴ 10 • written 3.4 years ago by ▴ 10
1
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3
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2.7k
views
ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest
DESeq2
updated 12 months ago by 43k • written 3.4 years ago by • 0
0
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1
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900
views
DESeq2 LRT not returning genes
LRT linearmodels DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 30
1
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2
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3.0k
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DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink DESeq2 RNASeq lfcthreshold
3.4 years ago ClaudiaE • 0
1
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12
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4.5k
views
How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 2.1 years ago by ★ 1.5k • written 3.4 years ago by • 0
1
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1
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662
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Error message : DESeq2
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
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1
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942
views
result does not change after relevel
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
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14
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6.2k
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GenomeInfoDbData had non-zero exit status
DESeq2 RStudio GenomeInfoDbData hadnon-zeroexitstatus
updated 3.2 years ago by • 0 • written 3.4 years ago by • 0
2
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2
replies
924
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DESeq2 question
DESeq2
3.4 years ago Yu • 0
0
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4
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1.5k
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Multi-factorial Time-based design in DEseq2: defining full and reduced model
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
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1
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805
views
how do singleton samples contribute to dispersion estimate in DESeq2?
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 10
1
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4
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7.2k
views
Error message: Could not find function "DESeqDataSetFromMatrix"
DESeq2
3.4 years ago Md. Faridul • 0
0
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1
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800
views
Error
DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
2
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8
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5.0k
views
How to get DESeq2 results for a list of genes
DESeq2
3.4 years ago Lucía ▴ 30
1
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1
reply
1.3k
views
setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
0
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4
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1.9k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
3.4 years ago uhlkatie • 0
4,840 results • Page 20 of 97
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Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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Popular Question to Hervé Pagès 16k
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