Showing : DESeq2 • reset
12
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[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
8
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10
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32k
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DESeq2 output explanation
deseq deseq2
updated 6.5 years ago by 32k • written 6.5 years ago by ▴ 60
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
20
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14
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24k
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deseq2 filter the low counts
deseq2 lowcount
updated 10 weeks ago by 32k • written 6.2 years ago by ▴ 30
8
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4
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23k
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DESeq2 baseMean counts
deseq2
updated 5.4 years ago by 32k • written 5.4 years ago by • 0
13
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4
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21k
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FDR and padj in deseq and edger
deseq2 edger
updated 5.5 years ago by 42k • written 5.5 years ago by ▴ 60
6
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5
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19k
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plotPCA - how to add labels to a PCA plot
plotPCA deseq2 labels
updated 4.3 years ago by ▴ 110 • written 4.3 years ago by ▴ 20
8
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10
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18k
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Design formula and Design matrix in DESeq
rnaseq deseq2 formula Limma
6.0 years ago AurelieMLB ▴ 50
12
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3
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16k
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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
1
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11
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16k
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With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 6.3 years ago by 32k • written 6.3 years ago by ▴ 20
2
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18
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16k
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DEseq2 time-series design.
deseq2 timecourse design
updated 22 months ago by • 0 • written 6.5 years ago by ▴ 90
3
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14
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16k
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Normalization in DESeq2
deseq2 deseq
updated 6.4 years ago by 32k • written 6.4 years ago by ▴ 70
5
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6
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15k
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Group comparison in DESeq2
deseq2 results
updated 5.7 years ago by 32k • written 5.7 years ago by ▴ 20
9
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6
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15k
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DESEq2 comparison with mulitple cell types under 2 conditions
deseq2 multiple factor design
updated 6.0 years ago by 32k • written 6.0 years ago by ▴ 40
4
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4
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15k
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Report and compare log2FC vs FC
deseq2 logfc
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by ▴ 60
13
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9
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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
7
votes
8
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14k
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Integrating DESeq2 and TopGO for Enrichment
go deseq2 rnaseq r
updated 6.2 years ago by ▴ 590 • written 6.2 years ago by ▴ 20
20
votes
12
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14k
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New function lfcShrink() in DESeq2
deseq2
updated 21 months ago by • 0 • written 4.0 years ago by 32k
0
votes
9
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13k
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logfoldStandard Error and wald-statistics in DESeq2 results
deseq2 wald
updated 6.2 years ago by 32k • written 6.2 years ago by ▴ 10
0
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4
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12k
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3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
deseq2 rnaseq PCA
updated 6.1 years ago by 32k • written 6.1 years ago by ▴ 50
13
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4
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12k
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Dealing with genes that have Padj=NA
deseq2
updated 2.8 years ago by ▴ 10 • written 5.4 years ago by ▴ 50
2
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3
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12k
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Removing genes with very low counts in all samples before run DESeq
deseq2 statistical power independent filtering
6.4 years ago alejandro.colaneri ▴ 20
1
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10
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12k
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Inputting counts of zero into DESeq2
deseq2
updated 5.9 years ago by ▴ 10 • written 6.4 years ago by ▴ 10
6
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15
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12k
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DESEq2 Paired samples Before and after treatment
deseq2 paired samples
4.9 years ago adesrichard ▴ 20
1
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7
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12k
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getting error with DEseq2
deseq2
5.0 years ago Nemo ▴ 80
11
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17
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11k
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DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
written 6.5 years ago by ▴ 120
23
votes
22
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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
6
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5
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11k
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Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 4.3 years ago by 25k • written 4.3 years ago by ▴ 10
1
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3
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11k
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log2FoldChange calculation in DESeq2 output
deseq2
updated 5.3 years ago by 32k • written 5.3 years ago by • 0
2
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4
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10k
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DESeq2 FPKM normalization
deseq2 normalization
5.2 years ago ribioinfo ▴ 90
10
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1
reply
10k
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Deseq2: RNA-seq and Negative binomial distribution
rnaseq deseq2
updated 5.5 years ago by 32k • written 5.5 years ago by ▴ 20
3
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6
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10k
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Unable to load library DESeq2 (installation of package had non-zero exit status)
DESeq2
updated 3.0 years ago by 32k • written 3.0 years ago by ▴ 30
5
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14
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10k
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DESeq2 paired multifactor test
deseq2 paired
6.5 years ago hwillenbrock ▴ 10
2
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5
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10k
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DESeq2: Paired Test
DESeq DESeq2 DESeq DESeq2
7.1 years ago • updated 7.0 years ago Pankaj Agarwal ▴ 100
26
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16
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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
3
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2
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9.6k
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DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2 R rnaseq
updated 5.3 years ago by 32k • written 5.3 years ago by • 0
18
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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
15
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8
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9.1k
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DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
6.5 years ago salahm ▴ 70
1
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1
reply
9.1k
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Deseq2 for RNAseq experiments without replicates
rnaseq deseq2
updated 5.3 years ago by 32k • written 5.3 years ago by • 0
8
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8
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9.0k
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Heatmap from DESeq2 DE genes
deseq2 heatmap
updated 6.3 years ago by 56k • written 6.3 years ago by ▴ 60
0
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1
reply
8.8k
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package DESeq2 installation with R.
deseq2 R package installation
updated 3.1 years ago by ▴ 160 • written 3.1 years ago by • 0
22
votes
7
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8.8k
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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
9
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9
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8.6k
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How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
6.3 years ago gavrielmatt • 0
2
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3
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8.5k
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DESeq2: multiple factors and comparison of a main factor between samples
deseq2 multiple factor design
updated 6.1 years ago by 32k • written 6.1 years ago by ▴ 80
2
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6
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8.4k
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DESeq2 vs limma/voom: PCA completely different. How to proceed?
limma DESeq2 limma DESeq2
updated 8.0 years ago by ★ 3.6k • written 8.0 years ago by ▴ 270
5
votes
11
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8.3k
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DESeq2: with multiple factors and interaction terms won't show all effects
deseq2 multiple factor design contrast interactions
updated 6.2 years ago by 32k • written 6.2 years ago by ▴ 80
1
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5
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8.3k
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How do I extract the principal components in DESeq2?
deseq2 pca
updated 5.8 years ago by 32k • written 5.8 years ago by ▴ 10
7
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3
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8.2k
views
DESeq2: multiple conditions design -- How to select subset comparisons from the DESeq object for PCA, ...
deseq2
updated 4.3 years ago by • 0 • written 5.1 years ago by ▴ 20
1
vote
1
reply
8.2k
views
Undertanding how DESeq2 handles multiple test conditions
rnaseq deseq2 r
updated 6.2 years ago by 7.6k • written 6.2 years ago by ▴ 20
3
votes
8
replies
8.1k
views
What is colData? How do I make one?
deseq2 coldata
updated 2.5 years ago by ▴ 710 • written 2.5 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
Scholar to Axel Klenk ▴ 980
Commentator to Steve Lianoglou 13k
Teacher to Aaron Lun ★ 26k
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