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DESeq2
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0
votes
1
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40
views
Adding gene names to DESeq result
DESeq2
updated 21 hours ago by
Basti
▴ 540 • written 1 day ago by
Chelsea
• 0
0
votes
1
reply
68
views
struggling to create a heatmap
DESeq2
heatmaps
updated 2 days ago by
ATpoint
★ 2.1k • written 3 days ago by
m-bihie
▴ 10
0
votes
1
reply
75
views
collapseReplicates error after tximeta
fishpond
tximeta
DESeq2
updated 3 days ago by
Michael Love
39k • written 4 days ago by
Rihards Saksis
• 0
0
votes
2
replies
79
views
Which genes are outliers in DESeq2?
DESeq2
RNAseq
outlier
updated 3 days ago by
ATpoint
★ 2.1k • written 3 days ago by
James
• 0
2
votes
2
replies
77
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2
SpikeIn
Normalization
DifferentialExpression
updated 3 days ago by
ATpoint
★ 2.1k • written 3 days ago by
kalavattam
▴ 10
3
votes
1
reply
56
views
log2 of normalized counts for further analyzes
DESeq2
log2
normalized
counts
updated 3 days ago by
James W. MacDonald
62k • written 3 days ago by
Laia
▴ 10
0
votes
2
replies
76
views
DESeq2 parameter infernce
DESeq2
7 days ago • updated 5 days ago
BioEpi
• 0
0
votes
1
reply
64
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2
LRT
continuous
coeficients
updated 6 days ago by
Michael Love
39k • written 7 days ago by
Laia
▴ 10
0
votes
1
reply
74
views
DESeq2 with sample effect, unequal sample sizes
DESeq2
updated 6 days ago by
Michael Love
39k • written 7 days ago by
rf
• 0
0
votes
1
reply
57
views
DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the library type when I using DESeq() function if I already using featur…
DESeq2
featurecounts
updated 7 days ago by
swbarnes2
★ 1.2k • written 7 days ago by
Bo
• 0
1
vote
1
reply
77
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 7 days ago by
ATpoint
★ 2.1k • written 7 days ago by
luca.s
▴ 40
0
votes
1
reply
62
views
RUVr batch correction doubling number of DEGs
DESeq2
RUVSeq
updated 8 days ago by
Michael Love
39k • written 8 days ago by
Zainab
• 0
0
votes
3
replies
1.3k
views
Which version of DESeq2 for R 4.1.2 64bit
DESeq2
written 12 months ago by
pam
• 0
3
votes
2
replies
85
views
I cannot install annotables package in Rstudio (macOS)
DESeq2
PackageTypeData
package
Annotation
11 days ago • updated 7 days ago
m-bihie
▴ 10
3
votes
5
replies
158
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 11 days ago by
Michael Love
39k • written 11 days ago by
aditya.m
▴ 10
0
votes
1
reply
89
views
DESeq2 in R 4.2.2
DESeq2
SummarizedExperiment
DelayedArray
updated 11 days ago by
ATpoint
★ 2.1k • written 12 days ago by
Danielle
• 0
0
votes
1
reply
96
views
Libraries loading error
DESeq2
clusterProfiler
enrichplot
updated 14 days ago by
Michael Love
39k • written 18 days ago by
joanna
• 0
0
votes
1
reply
111
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 14 days ago by
Michael Love
39k • written 14 days ago by
kalavattam
▴ 10
2
votes
2
replies
134
views
[DESeq2] There is no difference in expression in my heatmap
DESeq2
heatmaps
15 days ago • updated 13 days ago
Sooni
▴ 10
0
votes
1
reply
86
views
Extracting interaction contrast when using user supplied model.matrix
DESeq2
updated 16 days ago by
Michael Love
39k • written 17 days ago by
idetoma
• 0
1
vote
3
replies
205
views
DESeq2 Installation Issue
DESeq2
updated 18 days ago by
Hervé Pagès
16k • written 18 days ago by
joanna
• 0
2
votes
4
replies
145
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2
DifferentialExpression
updated 14 days ago by
Michael Love
39k • written 18 days ago by
idetoma
• 0
0
votes
1
reply
83
views
Rnaseq analysis using a continuous time series
DESeq2
updated 18 days ago by
Michael Love
39k • written 18 days ago by
Aviads
• 0
0
votes
2
replies
99
views
installing DESeq2 on Macbook R Studio
DESeq2
updated 18 days ago by
Michael Love
39k • written 18 days ago by
Chatura
• 0
0
votes
1
reply
63
views
More information on results columns
DESeq2
updated 18 days ago by
ATpoint
★ 2.1k • written 18 days ago by
krigerkoalaen
• 0
0
votes
1
reply
78
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2
RNASeqData
DifferentialExpression
updated 19 days ago by
ATpoint
★ 2.1k • written 19 days ago by
Julie
• 0
0
votes
3
replies
116
views
Do the count values should be only integer to be able to use DESeq2?
DESeq2
19 days ago
Sepehr
• 0
0
votes
5
replies
127
views
Error running DESeq2 on longitudinal data: Error in checkFullRank(modelMatrix)
DESeq2
longitudinal
updated 17 days ago by
swbarnes2
★ 1.2k • written 20 days ago by
sharvari gujja
▴ 40
0
votes
1
reply
125
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 20 days ago by
Dario Strbenac
★ 1.5k • written 22 days ago by
Hicham
• 0
4
votes
7
replies
219
views
DESeq2: Repetitive padj values?
DESeq2
updated 14 days ago by
Michael Love
39k • written 21 days ago by
vanbelj
▴ 20
0
votes
1
reply
130
views
Is this DESeq2 interactions design correct?
DESeq2
interactions
updated 23 days ago by
Michael Love
39k • written 24 days ago by
bhagyesh
• 0
0
votes
3
replies
185
views
how to iterate all comparisons in group with "coef =" ?
DESeq2
updated 14 days ago by
Michael Love
39k • written 24 days ago by
theodore.georgomanolis
• 0
0
votes
1
reply
155
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2
Transcriptomics
RNASeq
updated 25 days ago by
Michael Love
39k • written 28 days ago by
Jayesh Kumar
• 0
0
votes
1
reply
173
views
Help for RNA sequencing analysis with DESEQ2
DESeq2
star
differentiallyexpressed
updated 25 days ago by
Michael Love
39k • written 4 weeks ago by
nico
• 0
1
vote
3
replies
182
views
Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2
edgeR
rnaseqGene
updated 25 days ago by
Michael Love
39k • written 4 weeks ago by
vpl685
• 0
0
votes
1
reply
84
views
Combining VST counts for replicates
DESeq2
updated 25 days ago by
Michael Love
39k • written 26 days ago by
Jayesh Kumar
• 0
0
votes
1
reply
91
views
How to set threshold of padj value in DeSeq2
DESeq2
padj
default
updated 25 days ago by
James W. MacDonald
62k • written 25 days ago by
Serena
• 0
0
votes
1
reply
78
views
Differential RNA seq on TCGA set
DESeq2
RNASeqData
updated 26 days ago by
ATpoint
★ 2.1k • written 26 days ago by
SilverCat
• 0
0
votes
1
reply
63
views
rlog() transformation works only when using DESeqDataSet, not matrix
DESeq2
updated 26 days ago by
Michael Love
39k • written 26 days ago by
licheny
• 0
0
votes
2
replies
106
views
Differential expression between samples of the same group
DESeq2
27 days ago • updated 21 days ago
Oded
• 0
0
votes
1
reply
105
views
Missing transcript
DESeq2
tximport
salmon
updated 4 weeks ago by
ATpoint
★ 2.1k • written 4 weeks ago by
camilia.savitri
• 0
1
vote
3
replies
204
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
4 weeks ago
Alexandre
• 0
1
vote
4
replies
137
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
4 weeks ago
Iwan
• 0
0
votes
3
replies
150
views
Differential gene expression analysis with data matrix generated with RSEM
DESeq2
edgeR
4 weeks ago
ubjw24
• 0
1
vote
1
reply
98
views
Using the standard deviation of DESeq rlog transformed counts to identify genes for hierarchical clustering
DESeq2
updated 4 weeks ago by
ATpoint
★ 2.1k • written 4 weeks ago by
Josiah
• 0
1
vote
1
reply
121
views
Time series RNA-seq without conditions
DESeq2
updated 4 weeks ago by
ATpoint
★ 2.1k • written 4 weeks ago by
Dunois
• 0
2
votes
1
reply
120
views
Confused about tximport-DESeq2 setup
DESeq2
tximport
salmon
updated 4 weeks ago by
ATpoint
★ 2.1k • written 4 weeks ago by
Dunois
• 0
1
vote
3
replies
376
views
Manually calculating log2 fold change values from DESeq2 normalized counts
DESeq2
DifferentialExpression
5 weeks ago
Jayesh Kumar
• 0
0
votes
3
replies
152
views
Tissue Level Differential Expression Analysis
DESeq2
DifferentialExpression
differentialex
Pseudobulk
SingleCell
updated 5 weeks ago by
Michael Love
39k • written 5 weeks ago by
skanda.hebbale
• 0
0
votes
4
replies
246
views
suggest to report differential count estimate in DESeq2
DESeq2
5 weeks ago • updated 25 days ago
Yongqing
• 0
50 results • Page
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Comment: TCGA: clinical data and expression data
by
sharifnstu1203002m
• 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Jonathan Göke
▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
by
Gordon Smyth
47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user)
by
lalanis1
• 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma
by
Gordon Smyth
47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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