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Deseq2
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0
votes
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reply
31
views
struggling to create a heatmap
DESeq2
heatmaps
updated 2 hours ago by
ATpoint
★ 2.1k • written 12 hours ago by
m-bihie
▴ 10
0
votes
1
reply
52
views
collapseReplicates error after tximeta
fishpond
tximeta
DESeq2
updated 13 hours ago by
Michael Love
39k • written 1 day ago by
Rihards Saksis
• 0
0
votes
2
replies
50
views
Which genes are outliers in DESeq2?
DESeq2
RNAseq
outlier
updated 15 hours ago by
ATpoint
★ 2.1k • written 16 hours ago by
James
• 0
2
votes
2
replies
50
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2
SpikeIn
Normalization
DifferentialExpression
updated 15 hours ago by
ATpoint
★ 2.1k • written 18 hours ago by
kalavattam
▴ 10
1
vote
1
reply
32
views
log2 of normalized counts for further analyzes
DESeq2
log2
normalized
counts
updated 16 hours ago by
James W. MacDonald
62k • written 17 hours ago by
Laia
• 0
0
votes
2
replies
67
views
DESeq2 parameter infernce
DESeq2
4 days ago • updated 2 days ago
BioEpi
• 0
0
votes
1
reply
58
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2
LRT
continuous
coeficients
updated 3 days ago by
Michael Love
39k • written 4 days ago by
Laia
▴ 10
0
votes
1
reply
70
views
DESeq2 with sample effect, unequal sample sizes
DESeq2
updated 3 days ago by
Michael Love
39k • written 5 days ago by
rf
• 0
0
votes
1
reply
47
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 4 days ago by
swbarnes2
★ 1.2k • written 4 days ago by
Bo
• 0
1
vote
1
reply
71
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 4 days ago by
ATpoint
★ 2.1k • written 5 days ago by
luca.s
▴ 40
0
votes
1
reply
58
views
RUVr batch correction doubling number of DEGs
DESeq2
RUVSeq
updated 5 days ago by
Michael Love
39k • written 6 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
82
views
I cannot install annotables package in Rstudio (macOS)
DESeq2
PackageTypeData
package
Annotation
8 days ago • updated 4 days ago
m-bihie
▴ 10
3
votes
5
replies
150
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 8 days ago by
Michael Love
39k • written 9 days ago by
aditya.m
▴ 10
0
votes
1
reply
84
views
DESeq2 in R 4.2.2
DESeq2
SummarizedExperiment
DelayedArray
updated 9 days ago by
ATpoint
★ 2.1k • written 9 days ago by
Danielle
• 0
0
votes
1
reply
91
views
Libraries loading error
DESeq2
clusterProfiler
enrichplot
updated 11 days ago by
Michael Love
39k • written 15 days ago by
joanna
• 0
0
votes
1
reply
95
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 11 days ago by
Michael Love
39k • written 11 days ago by
kalavattam
▴ 10
2
votes
2
replies
129
views
[DESeq2] There is no difference in expression in my heatmap
DESeq2
heatmaps
12 days ago • updated 10 days ago
Sooni
▴ 10
0
votes
1
reply
83
views
Extracting interaction contrast when using user supplied model.matrix
DESeq2
updated 13 days ago by
Michael Love
39k • written 14 days ago by
idetoma
• 0
1
vote
3
replies
196
views
DESeq2 Installation Issue
DESeq2
updated 15 days ago by
Hervé Pagès
16k • written 15 days ago by
joanna
• 0
2
votes
4
replies
141
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2
DifferentialExpression
updated 11 days ago by
Michael Love
39k • written 16 days ago by
idetoma
• 0
0
votes
1
reply
80
views
Rnaseq analysis using a continuous time series
DESeq2
updated 15 days ago by
Michael Love
39k • written 16 days ago by
Aviads
• 0
0
votes
2
replies
94
views
installing DESeq2 on Macbook R Studio
DESeq2
updated 15 days ago by
Michael Love
39k • written 16 days ago by
Chatura
• 0
0
votes
1
reply
61
views
More information on results columns
DESeq2
updated 16 days ago by
ATpoint
★ 2.1k • written 16 days ago by
krigerkoalaen
• 0
0
votes
1
reply
74
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2
RNASeqData
DifferentialExpression
updated 16 days ago by
ATpoint
★ 2.1k • written 16 days ago by
Julie
• 0
0
votes
3
replies
110
views
Do the count values should be only integer to be able to use DESeq2?
DESeq2
17 days ago • updated 16 days ago
Sepehr
• 0
0
votes
5
replies
123
views
Error running DESeq2 on longitudinal data: Error in checkFullRank(modelMatrix)
DESeq2
longitudinal
updated 15 days ago by
swbarnes2
★ 1.2k • written 17 days ago by
sharvari gujja
▴ 40
0
votes
1
reply
121
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 18 days ago by
Dario Strbenac
★ 1.5k • written 19 days ago by
Hicham
• 0
4
votes
7
replies
216
views
DESeq2: Repetitive padj values?
DESeq2
updated 11 days ago by
Michael Love
39k • written 18 days ago by
vanbelj
▴ 20
0
votes
1
reply
127
views
Is this DESeq2 interactions design correct?
DESeq2
interactions
updated 20 days ago by
Michael Love
39k • written 21 days ago by
bhagyesh
• 0
0
votes
3
replies
183
views
how to iterate all comparisons in group with "coef =" ?
DESeq2
updated 11 days ago by
Michael Love
39k • written 21 days ago by
theodore.georgomanolis
• 0
0
votes
1
reply
145
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2
Transcriptomics
RNASeq
updated 22 days ago by
Michael Love
39k • written 25 days ago by
Jayesh Kumar
• 0
0
votes
1
reply
169
views
Help for RNA sequencing analysis with DESEQ2
DESeq2
star
differentiallyexpressed
updated 22 days ago by
Michael Love
39k • written 28 days ago by
nico
• 0
1
vote
3
replies
179
views
Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2
edgeR
rnaseqGene
updated 22 days ago by
Michael Love
39k • written 4 weeks ago by
vpl685
• 0
0
votes
1
reply
79
views
Combining VST counts for replicates
DESeq2
updated 22 days ago by
Michael Love
39k • written 23 days ago by
Jayesh Kumar
• 0
0
votes
1
reply
88
views
How to set threshold of padj value in DeSeq2
DESeq2
padj
default
updated 22 days ago by
James W. MacDonald
62k • written 22 days ago by
Serena
• 0
0
votes
1
reply
74
views
Differential RNA seq on TCGA set
DESeq2
RNASeqData
updated 23 days ago by
ATpoint
★ 2.1k • written 23 days ago by
SilverCat
• 0
0
votes
1
reply
60
views
rlog() transformation works only when using DESeqDataSet, not matrix
DESeq2
updated 23 days ago by
Michael Love
39k • written 23 days ago by
licheny
• 0
0
votes
2
replies
101
views
Differential expression between samples of the same group
DESeq2
24 days ago • updated 19 days ago
Oded
• 0
0
votes
1
reply
100
views
Missing transcript
DESeq2
tximport
salmon
updated 28 days ago by
ATpoint
★ 2.1k • written 29 days ago by
camilia.savitri
• 0
1
vote
3
replies
193
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
29 days ago • updated 28 days ago
Alexandre
• 0
1
vote
4
replies
134
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
4 weeks ago
Iwan
• 0
0
votes
3
replies
144
views
Differential gene expression analysis with data matrix generated with RSEM
DESeq2
edgeR
4 weeks ago • updated 29 days ago
ubjw24
• 0
1
vote
1
reply
94
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
115
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
117
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
369
views
Manually calculating log2 fold change values from DESeq2 normalized counts
DESeq2
DifferentialExpression
5 weeks ago • updated 4 weeks ago
Jayesh Kumar
• 0
0
votes
3
replies
149
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
240
views
suggest to report differential count estimate in DESeq2
DESeq2
5 weeks ago • updated 23 days ago
Yongqing
• 0
2
votes
2
replies
155
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
written 5 weeks ago by
kiqbal
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: struggling to create a heatmap
by
ATpoint
★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta
by
Michael Love
39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2?
by
Michael Love
39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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