Showing : deseq2 • reset
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
0
votes
7
replies
468
views
DESeq2 filtering vs edgeR filtering
DESeq2
10 weeks ago • updated 8 weeks ago fr8712ca-s • 0
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
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
0
votes
4
replies
760
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
12 months ago sreeshmaraj72 • 0
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 10 months ago by 66k • written 10 months ago by • 0
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
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
1
vote
2
replies
716
views
DESeq2 batch design
DESeq2
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 10
1
vote
8
replies
1.6k
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 11 months ago by • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
3
replies
491
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
6 months ago • updated 5 months ago Karthik • 0
0
votes
6
replies
930
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
7 months ago • updated 6 months ago erika.maldonado-rosado • 0
0
votes
3
replies
519
views
Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 8 months ago by 66k • written 8 months ago by ▴ 30
0
votes
2
replies
609
views
DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 5 months ago by 42k • written 5 months ago by • 0
0
votes
5
replies
721
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout DESeq2
written 11 months ago by • 0
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
1
vote
3
replies
446
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
0
votes
4
replies
404
views
Extract LRT results for each comparison
LRT DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
5
replies
575
views
Unexpected results for a differential expression analysis between males and females
DESeq2
updated 5 months ago by ★ 3.3k • written 5 months ago by • 0
1
vote
3
replies
517
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 5 months ago by • 0 • written 5 months ago by • 0
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
1
vote
3
replies
617
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 5 months ago by • 0
2
votes
2
replies
337
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
12 weeks ago Hope ▴ 10
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
0
votes
2
replies
570
views
Heat Map
ColData pheatmap DESeq2
written 11 months ago by • 0
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by ▴ 60
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
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 6 months ago by • 0 • written 6.6 years ago by ▴ 60
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
0
votes
6
replies
309
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 18 days ago by ★ 1.4k • written 19 days ago by ▴ 130
0
votes
3
replies
430
views
LOG2FC DESEQ2
DESeq2
updated 3 months ago by 42k • written 3 months ago by • 0
0
votes
2
replies
326
views
Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 10 months ago by 66k • written 10 months ago by • 0
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
1
vote
3
replies
1.8k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 4.2 years 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
10 months ago Ndimensional ▴ 20
2
votes
6
replies
3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 10 months ago by • 0 • written 8.1 years ago by ▴ 20
0
votes
2
replies
505
views
plotCounts label each sample
p DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
4
votes
7
replies
911
views
weird volcano plot
DESeq2
updated 11 weeks ago by • 0 • written 6 months ago by ▴ 10
0
votes
2
replies
353
views
Running DESeq on normalized data
deseq DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
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
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
10 months ago Luca • 0
0
votes
4
replies
296
views
DEG with low counts
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 7 months ago by • 0 • written 5.4 years ago by • 0
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
1
vote
3
replies
918
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
updated 11 months ago by • 0 • written 12 months ago by • 0
0
votes
2
replies
176
views
DESeq2 v1.35.0
DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
0
votes
17
replies
3.5k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 11 months ago by • 0 • written 6.7 years ago by • 0
2
votes
6
replies
392
views
Factor vs Character in design
DESeq2
11 weeks ago James Aiden • 0
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
11 months ago Ndimensional ▴ 20
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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