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DESeq2
•
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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
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
2
replies
183
views
DESeq2 v1.35.0
DESeq2
updated 21 days ago by
Michael Love
42k • written 21 days ago by
Espresso
• 0
0
votes
6
replies
312
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 19 days ago by
swbarnes2
★ 1.4k • written 21 days ago by
arfranco
▴ 130
1
vote
2
replies
771
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
5 weeks ago • updated 27 days ago
Patadù
▴ 10
1
vote
1
reply
199
views
Handling multiple differential expression comparisons
DESeq2
updated 18 days ago by
Michael Love
42k • written 20 days ago by
Zainab
▴ 10
0
votes
1
reply
193
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 13 days ago by
ATpoint
★ 4.2k • written 13 days ago by
sajadahmad41454
• 0
2
votes
3
replies
268
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 18 days ago by
ATpoint
★ 4.2k • written 20 days ago by
Reza
• 0
0
votes
6
replies
597
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
6 days ago • updated 3 days ago
Ken C
• 0
1
vote
3
replies
138
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 3 days ago by
James W. MacDonald
66k • written 4 days ago by
boczniak767
▴ 720
1
vote
8
replies
141
views
Slightly different count plots from R and spreadsheet
DESeq2
ggplot2
1 day ago
boczniak767
▴ 720
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 13 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
2
replies
28
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 1 hour ago by
Michael Love
42k • written 2 hours ago by
tjl
• 0
1
vote
4
replies
537
views
DEseq2 coefficient
DESeq2
coefficient
3 months ago • updated 22 days ago
JKim
• 0
3
votes
1
reply
337
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
i.sudbery
▴ 40
4
votes
9
replies
314
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 7 days ago by
ATpoint
★ 4.2k • written 8 days ago by
pangtaihin
• 0
1
vote
4
replies
366
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
29 days ago • updated 27 days ago
winwater0928
• 0
1
vote
3
replies
245
views
Different Shrunk Log2FC according with reference
DESeq2
updated 29 days ago by
Michael Love
42k • written 29 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
170
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 29 days ago by
Michael Love
42k • written 29 days ago by
kcarey
• 0
0
votes
2
replies
233
views
PCA plot suggestions
DESeq2
PCAtools
updated 27 days ago by
Michael Love
42k • written 28 days ago by
Aaliya
• 0
2
votes
9
replies
449
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 28 days ago by
James W. MacDonald
66k • written 28 days ago by
Alexandre
• 0
1
vote
3
replies
261
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 27 days ago by
Michael Love
42k • written 28 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
119
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 9 days ago by
Michael Love
42k • written 10 days ago by
piemmea
• 0
0
votes
8
replies
558
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 9 days ago by
BioinfGuru
▴ 30 • written 10 days ago by
Eric Katagirya
• 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
ATpoint
★ 4.2k • written 24 days ago by
bioinf
▴ 10
0
votes
1
reply
143
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 23 days ago by
Michael Love
42k • written 24 days ago by
Agung
• 0
0
votes
1
reply
120
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 14 days ago by
ATpoint
★ 4.2k • written 14 days ago by
sajadahmad41454
• 0
2
votes
4
replies
217
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 3 days ago by
Michael Love
42k • written 6 days ago by
shaunpeterson
• 0
0
votes
3
replies
154
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 8 days ago by
Michael Love
42k • written 9 days ago by
Kasper
• 0
1
vote
1
reply
162
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
marcusn
• 0
0
votes
3
replies
310
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 22 days ago by
Michael Love
42k • written 23 days ago by
HAK
• 0
1
vote
3
replies
320
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 15 days ago by
ATpoint
★ 4.2k • written 22 days ago by
angelathuynh5
• 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
22 days ago • updated 21 days ago
kcarey
• 0
0
votes
2
replies
177
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
23 days ago • updated 20 days ago
Aurora
• 0
0
votes
1
reply
143
views
putting my own expression data in deseq2
DESeq2
updated 23 days ago by
ATpoint
★ 4.2k • written 23 days ago by
Dev
• 0
2
votes
7
replies
443
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
15 days ago • updated 12 days ago
sajadahmad41454
• 0
1
vote
2
replies
271
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
10 days ago • updated 7 days ago
BioinfGuru
▴ 30
0
votes
3
replies
239
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 21 days ago by
ATpoint
★ 4.2k • written 22 days ago by
james.zhang20
• 0
0
votes
8
replies
410
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 28 days ago by
swbarnes2
★ 1.4k • written 4 weeks ago by
Aaliya
• 0
38 results • Page
1 of 1
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered"
by
Michael Love
42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
ATpoint
★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
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…
Votes
Answer: Documenting resources in an `ExperimentHub` package?
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
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★ 4.2k
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