Showing : DESeq2 • reset
13
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12
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[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 6.8 years ago by 13k • written 6.8 years ago by ▴ 110
11
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15
replies
36k
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DESeq2 output explanation
deseq deseq2
updated 10 weeks ago by 35k • written 7.2 years ago by ▴ 70
21
votes
14
replies
29k
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deseq2 filter the low counts
deseq2 lowcount
updated 11 months ago by 35k • written 6.9 years ago by ▴ 30
45
votes
20
replies
28k
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Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 5.6 years ago by • 0 • written 6.1 years ago by ▴ 100
8
votes
4
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26k
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DESeq2 baseMean counts
deseq2
updated 6.1 years ago by 35k • written 6.1 years ago by • 0
16
votes
4
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23k
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FDR and padj in deseq and edger
deseq2 edger
updated 6.2 years ago by 44k • written 6.2 years ago by ▴ 60
12
votes
5
replies
23k
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plotPCA - how to add labels to a PCA plot
plotPCA deseq2 labels
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by ▴ 50
15
votes
3
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21k
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DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 5.0 years ago by 35k • written 5.0 years ago by ▴ 40
8
votes
10
replies
20k
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Design formula and Design matrix in DESeq
rnaseq deseq2 formula Limma
6.7 years ago AurelieMLB ▴ 50
3
votes
11
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19k
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With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 7.0 years ago by 35k • written 7.0 years ago by ▴ 20
14
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9
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18k
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DESeq2 and shrinkage of log2 fold changes
deseq2
updated 12 months ago by 35k • written 6.0 years ago by ▴ 100
2
votes
18
replies
18k
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DEseq2 time-series design.
deseq2 timecourse design
updated 2.6 years ago by • 0 • written 7.2 years ago by ▴ 90
4
votes
8
replies
17k
views
What is colData? How do I make one?
deseq2 coldata
updated 3.2 years ago by ▴ 970 • written 3.2 years ago by ▴ 10
9
votes
6
replies
17k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2 multiple factor design
updated 6.7 years ago by 35k • written 6.7 years ago by ▴ 40
5
votes
4
replies
16k
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Report and compare log2FC vs FC
deseq2 logfc
updated 6.8 years ago by ▴ 10 • written 6.8 years ago by ▴ 70
20
votes
12
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16k
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New function lfcShrink() in DESeq2
deseq2
updated 2.4 years ago by • 0 • written 4.7 years ago by 35k
3
votes
14
replies
16k
views
Normalization in DESeq2
deseq2 deseq
updated 7.1 years ago by 35k • written 7.1 years ago by ▴ 70
5
votes
6
replies
16k
views
Group comparison in DESeq2
deseq2 results
updated 6.4 years ago by 35k • written 6.4 years ago by ▴ 20
7
votes
8
replies
16k
views
Integrating DESeq2 and TopGO for Enrichment
go deseq2 rnaseq r
updated 6.9 years ago by ▴ 600 • written 6.9 years ago by ▴ 20
7
votes
15
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14k
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DESEq2 Paired samples Before and after treatment
deseq2 paired samples
5.6 years ago adesrichard ▴ 20
2
votes
11
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14k
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logfoldStandard Error and wald-statistics in DESeq2 results
deseq2 wald
updated 10 weeks ago by 35k • written 6.9 years ago by ▴ 20
13
votes
4
replies
14k
views
Dealing with genes that have Padj=NA
deseq2
updated 3.5 years ago by ▴ 10 • written 6.1 years ago by ▴ 50
0
votes
5
replies
13k
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package DESeq2 installation with R.
deseq2 R package installation
updated 7 months ago by 35k • written 3.8 years ago by • 0
1
vote
3
replies
13k
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log2FoldChange calculation in DESeq2 output
deseq2
updated 6.0 years ago by 35k • written 6.0 years ago by • 0
11
votes
17
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13k
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DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
written 7.2 years ago by ▴ 120
1
vote
10
replies
13k
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Inputting counts of zero into DESeq2
deseq2
updated 6.6 years ago by ▴ 10 • written 7.2 years ago by ▴ 10
0
votes
4
replies
13k
views
3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
deseq2 rnaseq PCA
updated 6.8 years ago by 35k • written 6.8 years ago by ▴ 50
2
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3
replies
13k
views
Removing genes with very low counts in all samples before run DESeq
deseq2 statistical power independent filtering
7.2 years ago alejandro.colaneri ▴ 20
1
vote
7
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13k
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getting error with DEseq2
deseq2
5.7 years ago Nemo ▴ 80
23
votes
22
replies
12k
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DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 4.6 years ago by ▴ 100 • written 6.4 years ago by ▴ 170
5
votes
14
replies
12k
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DESeq2 paired multifactor test
deseq2 paired
7.2 years ago hwillenbrock ▴ 10
3
votes
6
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12k
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Designing a contrast in DESEQ
deseq2 design and contrast matrix model matrix
4.9 years ago mrigaya.mehra ▴ 10
6
votes
5
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12k
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Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 5.0 years ago by 25k • written 5.0 years ago by ▴ 10
27
votes
16
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11k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 3.7 years ago by ▴ 10 • written 5.5 years ago by ▴ 170
10
votes
1
reply
11k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq deseq2
updated 6.2 years ago by 35k • written 6.2 years ago by ▴ 20
2
votes
5
replies
11k
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DESeq2: Paired Test
DESeq DESeq2 DESeq DESeq2
7.8 years ago • updated 7.7 years ago Pankaj Agarwal ▴ 100
2
votes
4
replies
11k
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DESeq2 FPKM normalization
deseq2 normalization
6.0 years ago • updated 5.9 years ago ribioinfo ▴ 100
18
votes
24
replies
11k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 11 months ago by • 0 • written 6.9 years ago by ▴ 110
3
votes
6
replies
11k
views
Unable to load library DESeq2 (installation of package had non-zero exit status)
DESeq2
updated 3.7 years ago by 35k • written 3.7 years ago by ▴ 40
2
votes
3
replies
10k
views
Contrast for DESeq2 design with interaction and blocking factor
deseq2
2.6 years ago erwan.scaon ▴ 10
3
votes
2
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9.9k
views
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2 R rnaseq
updated 6.0 years ago by 35k • written 6.0 years ago by • 0
10
votes
7
replies
9.9k
views
DESeq2: multiple conditions design -- How to select subset comparisons from the DESeq object for PCA, ...
deseq2
updated 11 weeks ago by 35k • written 5.8 years ago by ▴ 20
10
votes
9
replies
9.8k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
7.0 years ago gavrielmatt ▴ 10
22
votes
7
replies
9.8k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 5.3 years ago by ★ 3.7k • written 5.3 years ago by ▴ 20
1
vote
1
reply
9.7k
views
Deseq2 for RNAseq experiments without replicates
rnaseq deseq2
updated 6.0 years ago by 35k • written 6.0 years ago by • 0
3
votes
7
replies
9.6k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 2.9 years ago by 35k • written 2.9 years ago by • 0
8
votes
8
replies
9.5k
views
Heatmap from DESeq2 DE genes
deseq2 heatmap
updated 7.0 years ago by 58k • written 7.0 years ago by ▴ 70
15
votes
8
replies
9.5k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
7.2 years ago salahm ▴ 70
2
votes
6
replies
9.1k
views
DESeq2 vs limma/voom: PCA completely different. How to proceed?
limma DESeq2 limma DESeq2
updated 8.7 years ago by ★ 3.7k • written 8.7 years ago by ▴ 270
28
votes
17
replies
9.1k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
7.3 years ago • updated 5.8 years ago Michael Love 35k
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to get all possible comparisons in DiffBind by Rory Stark ★ 4.3k
Note that contrasts are handled differently since `DiffBind_3.0`. You can still calculate results for multiple contrasts simultaneously, bu…
Answer: Change the interval of bed file by James W. MacDonald 58k
How about ``` > library(GenomicRanges) ## reproducibility > set.seed(0xabeef) ## fake GRranges with scores > gr <- GRanges(rep("chr…
Comment: Uniform window size for different genes by James W. MacDonald 58k
OK, maybe I don't understand at all. From your original post I thought you wanted a single representative 'gene' rather than all the transc…
Comment: Uniform window size for different genes by rbenel ▴ 20
I tried some workaround, displaying the same gene on both tracks and playing with the `heights` but I still can't get the gene model to be …
Comment: Limma prametrization by Giovanni • 0
Thank you!
Votes
A: How to get all possible comparisons in DiffBind
Answer: Limma prametrization
Comment: Limma prametrization
A: Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
Answer: Unable to GetGRangesFromEnsDb
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