Showing : DEseq2 • reset
13
votes
22
replies
26k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 9 weeks ago by 41k • written 7.8 years ago by ▴ 30
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.2 years ago by ▴ 40
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 4 months ago by • 0 • written 2.2 years ago by • 0
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 10 months ago by • 0 • written 6.6 years ago by • 0
2
votes
17
replies
1.7k
views
lfcshrink error DESeq2
DESeq2 lfcshrink DESe
updated 11 months ago by 41k • written 11 months ago by • 0
3
votes
16
replies
2.1k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 3 months ago by 3.8k • written 2.8 years ago by ▴ 10
6
votes
16
replies
2.3k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by 41k • written 4.6 years ago by ▴ 10
8
votes
15
replies
1.4k
views
PCA percent variance DESeq2
PCA DESeq2
8 months ago • updated 7 months ago IUH • 0
5
votes
15
replies
5.0k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 10 months ago by 65k • written 6.8 years ago by ▴ 10
1
vote
15
replies
8.1k
views
Exporting DESeq2 filtered results
DESeq2
updated 6 months ago by 65k • written 3.2 years ago by ▴ 10
1
vote
13
replies
878
views
Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions replicates SmallRNAData DESeq2
updated 3 months ago by ★ 3.9k • written 4 months ago by ▴ 10
0
votes
13
replies
667
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2 SmallRNA
updated 8 weeks ago by 41k • written 9 weeks ago by • 0
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 7 days ago by • 0 • written 8.8 years ago by ▴ 30
3
votes
12
replies
2.1k
views
t.test to determine the P-value in DESeq2
DESeq2
written 18 months ago by • 0
8
votes
12
replies
2.5k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by 41k • written 12 months ago by ▴ 90
1
vote
12
replies
1.0k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
9 weeks ago • updated 8 weeks ago paria.alipour • 0
2
votes
12
replies
1.3k
views
P-value inflation?
DESeq2
updated 8 months ago by 65k • written 8 months ago by ▴ 10
1
vote
12
replies
2.7k
views
How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 6 months ago by ★ 1.5k • written 21 months ago by • 0
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
6
votes
11
replies
3.9k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 6 weeks ago by • 0 • written 3.2 years ago by ▴ 40
1
vote
11
replies
997
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 8 months ago by • 0 • written 9.2 years ago by ▴ 40
2
votes
10
replies
1.1k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago • updated 5 months ago rohitsatyam102 ▴ 20
2
votes
10
replies
3.2k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 6 months ago by 41k • written 5.7 years ago by ▴ 20
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 5 months ago by • 0 • written 6.5 years ago by ▴ 60
0
votes
9
replies
1.4k
views
Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin DESeq2
updated 6 months ago by ▴ 10 • written 21 months ago by ▴ 10
4
votes
9
replies
4.3k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 11 months ago by • 0 • written 6.8 years ago by • 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
2
votes
9
replies
257
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 16 hours ago by 65k • written 1 day ago by • 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
9 months ago Ndimensional ▴ 20
4
votes
9
replies
1.2k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
1
vote
9
replies
5.3k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.1 years ago by • 0
1
vote
9
replies
868
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
0
votes
9
replies
1.3k
views
ranking the DeSeq2 results using t-values?
DESeq2
updated 10 months ago by 41k • written 10 months ago by ▴ 10
0
votes
9
replies
830
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
8 months ago mjd275 • 0
8
votes
8
replies
9.7k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 7 months ago by • 0 • written 4.8 years ago by ▴ 40
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 25 days ago by ★ 13k • written 10 months ago by ▴ 10
1
vote
8
replies
1.5k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 10 months ago by • 0
0
votes
8
replies
801
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
5 months ago Luca • 0
0
votes
8
replies
379
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
7 weeks ago michelafrancesconi8 • 0
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
10 months ago Ndimensional ▴ 20
1
vote
8
replies
2.7k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.1 years ago by ▴ 60
1
vote
8
replies
2.5k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 4 months ago by • 0 • written 3.3 years ago by ▴ 10
0
votes
8
replies
704
views
Deseq2 Results are different using batch design
DESeq2
9 months ago hemantcnaik • 0
4
votes
8
replies
2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 17 months ago by ▴ 20
0
votes
8
replies
237
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 1 day ago by ★ 1.3k • written 2 days ago by • 0
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 6 months ago by ▴ 10 • written 6.5 years ago by ▴ 30
4
votes
7
replies
842
views
weird volcano plot
DESeq2
updated 7 weeks ago by • 0 • written 5 months ago by ▴ 10
8
votes
7
replies
1.7k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 9 months ago by ▴ 20 • written 18 months ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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