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 4 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
928
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 22 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
923
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
303
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 6 days ago by ★ 4.1k • written 7 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
241
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
903
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
3
votes
3
replies
276
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 23 days ago by ★ 4.1k • written 23 days ago by ▴ 10
3
votes
6
replies
864
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
918
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
331
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 28 days ago by 42k • written 29 days ago by ▴ 40
3
votes
3
replies
257
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 29 days 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
898
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
3
votes
3
replies
582
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
432
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
676
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 11 weeks ago by 42k • written 12 weeks ago by ▴ 10
3
votes
2
replies
592
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 6.4 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
Answer: Help with infinite recursion - non-zero exit status in installation of GenomeInf by James W. MacDonald 66k
Maybe just try again? ``` > install("GenomeInfoDbData", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositorie…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf by Brandon • 0
Hello, As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what …
Comment: slingshot: error with plot3d.SlingshotDataSet by Kelly Street • 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Comment: Slightly different count plots from R and spreadsheet by Michael Love 42k
Change timepoint to an integer in the data frame: ``` as.numeric(as.character( <factor> )) ``` Then it should make points instead of boxe…
Answer: WGNCA kME vs. kIM by Vitor • 0
You can compare kIM and kME within module assignments. The plot below is for my network (I used Pearson correlation and signed network). !…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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