Showing : deseq2 • reset
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
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 10 weeks ago by 41k • written 7.9 years ago by ▴ 30
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 16 days ago by • 0 • written 8.8 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 8.2 years ago by ▴ 90
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 18 months ago by ▴ 20
8
votes
12
replies
2.6k
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
8
votes
15
replies
1.5k
views
PCA percent variance DESeq2
PCA DESeq2
8 months ago IUH • 0
8
votes
8
replies
9.8k
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
7
votes
3
replies
883
views
Proper way to implement DESeq2 when comparing samples with trisomies?
DESeq2
updated 9 months ago by 41k • written 10 months ago by ▴ 20
7
votes
4
replies
2.8k
views
Normalized counts of DESeq2 affected by design formula?
deseq2
updated 3 months ago by • 0 • written 6.2 years ago by ▴ 20
6
votes
5
replies
4.1k
views
DESeq2: Extremely low pvalues
deseq2
updated 10 months ago by 65k • written 7.8 years ago by ▴ 20
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
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 7 weeks ago by • 0 • written 3.2 years ago by ▴ 40
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 4 days ago by • 0 • written 4.6 years ago by ▴ 10
5
votes
2
replies
869
views
can't install DESeq2 ("unable to access index for repository")
biocmanager DESeq2
8 months ago Alessia ▴ 40
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 3 months ago by 50k • written 13 months ago by • 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
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 2.3 years ago by • 0
4
votes
6
replies
2.3k
views
DESeq2 for single cell pseudobulk processing
DESeq2
updated 11 months ago by 41k • written 12 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 11 months ago by 50k • written 17 months ago by ▴ 20
4
votes
9
replies
4.4k
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
4
votes
13
replies
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
4
votes
7
replies
868
views
weird volcano plot
DESeq2
updated 8 weeks ago by • 0 • written 5 months ago by ▴ 10
4
votes
7
replies
700
views
DESeq2 unable to handle large count values
DESeq2
updated 6 weeks ago by 41k • written 5 months ago by • 0
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
4
votes
4
replies
1.1k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 7 weeks ago by • 0 • written 13 months ago by ▴ 10
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
3
votes
3
replies
976
views
Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 17 months ago by • 0
3
votes
6
replies
2.7k
views
DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 10 weeks ago by • 0 • written 5.2 years ago by ▴ 50
3
votes
12
replies
2.1k
views
t.test to determine the P-value in DESeq2
DESeq2
written 18 months ago by • 0
3
votes
1
reply
308
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 11 days ago by 41k • written 11 days ago by ▴ 40
3
votes
2
replies
675
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
5
replies
866
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
3
votes
6
replies
842
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
6
replies
22k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 3 months ago by • 0 • written 5.6 years ago by • 0
3
votes
3
replies
223
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 11 days ago by 41k • written 12 days ago by • 0
3
votes
3
replies
955
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by ▴ 20
3
votes
4
replies
874
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago • updated 8 months ago Eva ▴ 10
3
votes
1
reply
621
views
Applying DESeq2 to (suspected) Poisson distributed gene expression data (in the case of pseudoreplication)
DESeq2
updated 11 months ago by 41k • written 11 months ago by • 0
3
votes
5
replies
1.3k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 9 months ago by 41k • written 10 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 8 months ago by ★ 3.9k • written 8 months ago by ▴ 10
3
votes
2
replies
357
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 12 weeks ago by ▴ 30 • written 12 weeks ago by • 0
3
votes
3
replies
547
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
7 months ago Nisha • 0
3
votes
16
replies
2.1k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 3 months ago by 3.9k • written 2.8 years ago by ▴ 10
3
votes
2
replies
561
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
3
votes
2
replies
214
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
5 weeks ago Anita ▴ 10
3
votes
5
replies
625
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 10 weeks ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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