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Showing :
DESeq2
•
reset
5
votes
3
replies
27k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 6.2 years ago by
aishu.jp
▴ 30
38
votes
23
replies
17k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
10.5 years ago • updated 2 days ago
Michael Love
43k
5
votes
29
replies
5.2k
views
DESeq2 model - How to test case/control time course model when taking account within sample variability?
deseq2
multiple time points
time course
casecontrol
model design
updated 2 days ago by
Michael Love
43k • written 7.7 years ago by
heikki.sarin
▴ 10
1
vote
3
replies
4.5k
views
Log2 fold change value in DESeq2
deseq2
rnaseq
written 7.4 years ago by
AP
• 0
1
vote
5
replies
3.9k
views
DESeq2 swap ensembl gene id rownames with gene symbol column
deseq2
dataframe
ensembl gene id
gene symbol
entrezid
updated 9 days ago by
Erika
• 0 • written 5.3 years ago by
jason.williams
▴ 10
3
votes
7
replies
2.0k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 24 days ago by
melissa
▴ 10 • written 6.0 years ago by
david.wheeler7
▴ 20
0
votes
6
replies
2.0k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2
design
interaction term
R
written 7.1 years ago by
briverog
• 0
1
vote
6
replies
1.9k
views
how to analysis htseq-count
deseq2
written 7.2 years ago by
Bioinformatics
▴ 30
2
votes
4
replies
1.6k
views
deseq2 lfc shrinkage with few DEGs
RNASeq
DESeq2
updated 2 days ago by
Michael Love
43k • written 2.8 years ago by
Victor
▴ 10
2
votes
6
replies
1.5k
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 21 days ago by
Jane
• 0 • written 10 months ago by
Reza
• 0
1
vote
2
replies
1.2k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
12 days ago • updated 11 days ago
Luca
• 0
2
votes
5
replies
980
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
25 days ago • updated 24 days ago
picasa1983
• 0
4
votes
5
replies
928
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 4 days ago by
Esperan
• 0 • written 17 days ago by
Elijah
• 0
1
vote
1
reply
659
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2
org.Rn.eg.db
updated 9 days ago by
James W. MacDonald
68k • written 9 days ago by
Erika
• 0
0
votes
3
replies
601
views
how many significant figures are there in DESeq2 output
DESeq2
updated 21 days ago by
ATpoint
★ 4.7k • written 22 days ago by
Matthew McCormack
▴ 180
2
votes
2
replies
508
views
Plot title for PCA in DESeq2
DESeq2
29 days ago • updated 26 days ago
AL
• 0
1
vote
1
reply
452
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 27 days ago by
swbarnes2
★ 1.4k • written 27 days ago by
Len
▴ 10
0
votes
3
replies
448
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 26 days ago by
Leonard
• 0 • written 6 weeks ago by
Martijn
• 0
0
votes
4
replies
395
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2
TechnicalReplicates
RNASeq
written 5 days ago by
questionanswer
• 0
0
votes
2
replies
390
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 6 days ago by
Michael Love
43k • written 14 days ago by
rohitsatyam102
▴ 20
0
votes
1
reply
326
views
How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData
DESeq2
pseudobulk
sing
updated 26 days ago by
James W. MacDonald
68k • written 26 days ago by
Sara
• 0
1
vote
1
reply
286
views
DEseq2 design for additive treatment
DESeq2
updated 27 days ago by
ATpoint
★ 4.7k • written 28 days ago by
picasa1983
• 0
1
vote
3
replies
278
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
updated 3 days ago by
James W. MacDonald
68k • written 3 days ago by
Lennie
• 0
0
votes
1
reply
181
views
DESeq use in lipidomic analysis
DESeq2
package
Lipidomics
updated 17 days ago by
Michael Love
43k • written 18 days ago by
泓宇
• 0
24 results • Page
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Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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