Showing : DESeq2 • reset
44
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20
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25k
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Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 4.9 years ago by • 0 • written 5.4 years ago by ▴ 100
26
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16
replies
9.9k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 3.0 years ago by ▴ 10 • written 4.8 years ago by ▴ 160
25
votes
11
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5.7k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 5.5 years ago by ★ 3.6k • written 5.5 years ago by ▴ 70
24
votes
17
replies
7.9k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
6.6 years ago • updated 5.1 years ago Michael Love 32k
23
votes
22
replies
11k
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DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 3.8 years ago by ▴ 100 • written 5.7 years ago by ▴ 160
22
votes
7
replies
8.8k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 4.6 years ago by ★ 3.6k • written 4.6 years ago by ▴ 20
20
votes
14
replies
24k
views
deseq2 filter the low counts
deseq2 lowcount
updated 10 weeks ago by 32k • written 6.2 years ago by ▴ 30
20
votes
12
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14k
views
New function lfcShrink() in DESeq2
deseq2
updated 21 months ago by • 0 • written 4.0 years ago by 32k
18
votes
24
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9.6k
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[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 12 weeks ago by • 0 • written 6.1 years ago by ▴ 100
18
votes
12
replies
2.0k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 5.9 years ago by 32k • written 5.9 years ago by 7.6k
16
votes
9
replies
4.0k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 3.5 years ago by ★ 3.8k • written 5.1 years ago by ▴ 60
16
votes
11
replies
2.4k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 22 months ago by • 0 • written 2.9 years ago by ▴ 20
15
votes
12
replies
1.1k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 2.7 years ago by 32k • written 2.7 years ago by ▴ 60
15
votes
4
replies
1.4k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 4.9 years ago by 7.6k • written 4.9 years ago by ▴ 130
15
votes
8
replies
9.1k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
6.5 years ago salahm ▴ 70
14
votes
7
replies
3.2k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
14
votes
7
replies
6.0k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2 ensembl
updated 3.3 years ago by 56k • written 3.3 years ago by ▴ 130
13
votes
17
replies
7.0k
views
DESeq2 Model Design
DESeq2 linear model model
updated 6.4 years ago by 56k • written 6.5 years ago by ▴ 340
13
votes
9
replies
15k
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DESeq2 and shrinkage of log2 fold changes
deseq2
updated 3 months ago by 32k • written 5.3 years ago by ▴ 90
13
votes
25
replies
1.3k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 1 day ago by 32k • written 21 months ago by ▴ 30
13
votes
16
replies
3.0k
views
Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR deseq2 ase allele
5.6 years ago trianglescout ▴ 40
13
votes
10
replies
2.3k
views
Big differences in logfoldchange for some genes between edgeR and DESeq2
edger deseq2
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
13
votes
4
replies
12k
views
Dealing with genes that have Padj=NA
deseq2
updated 2.8 years ago by ▴ 10 • written 5.4 years ago by ▴ 50
13
votes
4
replies
21k
views
FDR and padj in deseq and edger
deseq2 edger
updated 5.5 years ago by 42k • written 5.5 years ago by ▴ 60
12
votes
11
replies
2.2k
views
Memory usage for bplapply -- is the entire environment copied over to each worker thread?
bplapply biocparallel deseq2
updated 5.8 years ago by ★ 6.7k • written 5.8 years ago by ▴ 40
12
votes
12
replies
42k
views
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 6.1 years ago by 13k • written 6.1 years ago by ▴ 100
12
votes
7
replies
2.5k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 4.9 years ago by 7.6k • written 4.9 years ago by • 0
12
votes
6
replies
2.0k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq deseq2 edger
5.4 years ago martiningi ▴ 40
12
votes
8
replies
938
views
DESeq fitted values using coefficients vs mu
deseq2
updated 4.3 years ago by 32k • written 4.3 years ago by ▴ 830
12
votes
3
replies
16k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 4.3 years ago by 32k • written 4.3 years ago by ▴ 30
11
votes
1
reply
3.1k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 3.5 years ago by 32k • written 3.5 years ago by ▴ 60
11
votes
8
replies
5.8k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 4.6 years ago by ★ 2.6k • written 4.6 years ago by ▴ 70
11
votes
17
replies
11k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
written 6.5 years ago by ▴ 120
10
votes
6
replies
3.5k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 3.6 years ago by 56k • written 3.6 years ago by ▴ 10
10
votes
9
replies
868
views
Overriding of shrinkage in DESeq2
deseq2
updated 5.1 years ago by 32k • written 5.1 years ago by ▴ 70
10
votes
9
replies
7.8k
views
DESeq2 baseMean values for each sample
deseq2
6.4 years ago aburkha69 ▴ 30
10
votes
6
replies
2.9k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq deseq2 edger voom limma
updated 3.6 years ago by ▴ 90 • written 5.9 years ago by 21k
10
votes
1
reply
10k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq deseq2
updated 5.5 years ago by 32k • written 5.5 years ago by ▴ 20
10
votes
7
replies
6.5k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 3.8 years ago by 32k • written 3.8 years ago by • 0
10
votes
14
replies
1.9k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 3.6 years ago by 42k • written 3.6 years ago by ▴ 70
9
votes
6
replies
1.1k
views
Independent filtering with unequal group sizes?
independent filtering edger deseq2
updated 5.8 years ago by ★ 26k • written 5.8 years ago by 7.6k
9
votes
10
replies
1.3k
views
Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a transcriptome?
deseq2 nanopore
2.0 years ago • updated 24 months ago David Eccles (gringer) ▴ 20
9
votes
9
replies
8.6k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
6.3 years ago gavrielmatt • 0
9
votes
14
replies
4.9k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
4.8 years ago • updated 4.7 years ago anand_mt ▴ 80
9
votes
17
replies
616
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 3.4 years ago by 32k • written 3.4 years ago by ▴ 60
9
votes
8
replies
7.7k
views
DEseq2 extended to open chromatin anlaysis: normalization, dispersion fit, and "too many" differences
deseq2 dnaseq
updated 6.6 years ago by 32k • written 6.6 years ago by ▴ 100
9
votes
7
replies
7.3k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 3.9 years ago by ▴ 10 • written 3.9 years ago by ▴ 30
9
votes
11
replies
6.3k
views
Normalization using DESeq
normalization deseq2
4.3 years ago aangajala ▴ 20
9
votes
6
replies
4.7k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 5.3 years ago by 32k • written 5.3 years ago by ▴ 270
9
votes
1
reply
1.7k
views
How to explain how DESeq2 works to someone with zero bioinformatics background?
deseq2
updated 4.0 years ago by 32k • written 4.0 years ago by • 0
3,403 results • Page 1 of 69
Recent ...
Replies
Comment: Limma paired analysis design question by jefflincoln4 • 0
Thank you Gordon. One more thing, why use the log of blood iron concentration?
Answer: Limma paired analysis design question by Gordon Smyth 42k
Just put (log) blood iron concentration and `pair` in the design matrix. limma will work with differences automatically -- there's no need…
Comment: Extracting the findPalindrome() results by Hervé Pagès 14k
Also, you have a point: the output of `Biostrings::findPalindromes()` is an XStringViews object and `as.data.frame()` does a poor job on th…
Comment: Compute fgsea with my own database with R version 4.0.2 by assaron ▴ 190
I'm not sure what would be the best course of action in your case, if there is one at all, but I'd suggest to keep the ranking on the gene-…
Comment: Error installing Deseq2 by ATpoint ▴ 590
Go through the error logs and find the first error, this is where you have to start debugging, this here is just the consequences of the in…
Votes
Comment: DESeq2 with high range of within-group variability
Comment: problem regarding differential gene express analysis
Comment: Normalisation in DESeq2
Answer: Compute fgsea with my own database with R version 4.0.2
Comment: lmFit, number of proteins
Awards • All
Popular Question to Gordon Smyth 42k
Scholar to James W. MacDonald 56k
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Teacher to Aaron Lun ★ 26k
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