Showing : deseq2 • reset
28
votes
21
replies
49k
views
deseq2 filter the low counts
deseq2 lowcount
updated 4 months ago by • 0 • written 9.2 years ago by ▴ 40
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 7 months ago by ▴ 10 • written 6.6 years ago by ▴ 30
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by • 0 • written 8.4 years ago by ▴ 60
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 3 months ago by 42k • written 7.9 years ago by ▴ 30
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.3 years ago by ▴ 90
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 weeks ago by • 0 • written 8.9 years ago by ▴ 30
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 19 months ago by ▴ 20
8
votes
8
replies
9.9k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 8 months ago by • 0 • written 4.8 years ago by ▴ 40
8
votes
15
replies
1.6k
views
PCA percent variance DESeq2
PCA DESeq2
9 months ago • updated 8 months ago IUH • 0
7
votes
3
replies
929
views
Proper way to implement DESeq2 when comparing samples with trisomies?
DESeq2
updated 10 months ago by 42k • written 10 months ago by ▴ 20
7
votes
4
replies
2.8k
views
Normalized counts of DESeq2 affected by design formula?
deseq2
updated 4 months ago by • 0 • written 6.2 years ago by ▴ 20
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 23 days ago by • 0 • written 4.6 years ago by ▴ 10
6
votes
11
replies
4.1k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 10 weeks ago by • 0 • written 3.2 years ago by ▴ 40
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 9 months ago by • 0 • written 9.3 years ago by ▴ 40
6
votes
5
replies
4.2k
views
DESeq2: Extremely low pvalues
deseq2
updated 10 months ago by 66k • written 7.8 years ago by ▴ 20
5
votes
2
replies
939
views
can't install DESeq2 ("unable to access index for repository")
biocmanager DESeq2
9 months ago Alessia ▴ 40
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 4 months ago by 50k • written 14 months ago by • 0
5
votes
15
replies
5.1k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 11 months ago by 66k • written 6.9 years ago by ▴ 10
5
votes
18
replies
7.6k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 5 months ago by • 0 • written 2.3 years ago by • 0
4
votes
9
replies
313
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 7 days ago by ★ 4.2k • written 8 days ago by • 0
4
votes
4
replies
1.2k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 9 weeks ago by • 0 • written 13 months ago by ▴ 10
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
10 months ago Luca • 0
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
4
votes
13
replies
1.5k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 42k • written 8 months ago by • 0
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 12 months ago by 50k • written 17 months ago by ▴ 20
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago Luca • 0
4
votes
7
replies
911
views
weird volcano plot
DESeq2
updated 11 weeks ago by • 0 • written 6 months ago by ▴ 10
4
votes
7
replies
742
views
DESeq2 unable to handle large count values
DESeq2
updated 9 weeks ago by 42k • written 6 months ago by • 0
3
votes
7
replies
910
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
9 months ago casco ▴ 10
3
votes
2
replies
244
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
8 weeks ago Anita ▴ 10
3
votes
5
replies
906
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.2k • written 8 months ago by • 0
3
votes
3
replies
279
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 24 days ago by ★ 4.2k • written 24 days ago by ▴ 10
3
votes
6
replies
865
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
votes
5
replies
922
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
3
votes
1
reply
335
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by ▴ 40
3
votes
3
replies
262
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
3
votes
12
replies
2.2k
views
t.test to determine the P-value in DESeq2
DESeq2
written 19 months ago by • 0
3
votes
2
replies
1.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
3
votes
6
replies
23k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 4 months ago by • 0 • written 5.7 years ago by • 0
3
votes
16
replies
2.2k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 4 months ago by 3.9k • written 2.9 years ago by ▴ 10
3
votes
4
replies
899
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
3
votes
3
replies
583
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
8 months ago Nisha • 0
3
votes
5
replies
1.4k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
3
votes
2
replies
434
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 3 months ago by ▴ 30 • written 3 months ago by • 0
3
votes
6
replies
2.8k
views
DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 3 months ago by • 0 • written 5.3 years ago by ▴ 50
3
votes
5
replies
678
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 11 weeks ago by 42k • written 12 weeks ago by ▴ 10
3
votes
2
replies
593
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 66k • written 5 months ago by • 0
3
votes
2
replies
690
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 11 months ago by 50k • written 11 months ago by ▴ 10
2
votes
2
replies
4.2k
views
choosing the normalization method (rlog, variance stabilizing transformation)
variancestabilizingtransformation rlog transformation deseq2
updated 6 months ago by • 0 • written 6.5 years ago by ▴ 80
2
votes
3
replies
1.2k
views
DESeq2: DE Analysis with very imbalanced samples per condition
deseq2 cancer
updated 4 months ago by • 0 • written 4.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Using the plotting functions of clusterProfiler / enrichplot with enrichment res by jovel_juan ▴ 30
enrichPlot requirements are rather low. All what it needs is to provide few columns named specifically. I student of mine wrote the first v…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by ATpoint ★ 4.2k
SAF files must not have a header.
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman by xuz • 0
Could you try the latest version (1.40.1) to see how it works, I am not able to replicate the error message on my computer here.
Comment: Not able to install any Bioconductor 3.18 package [unable to access index] by merv ▴ 120
Thanks! I can confirm it is working now - had been broken since sometime yesterday.
Comment: Errors in chromosome annotation-biomaRt by landenshanie ▴ 40
Thank you, I ran your exact code and it correct for Xist, however Ddx3y is still wrongly annotated to chr13 and, like your results, Dusp1 i…
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
Error when converting Seurat to SingleCellExperiment
Comment: unable to access bioconductor packages - qvalue installation failed...
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