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DeSeq2
•
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2
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2
replies
1.2k
views
[DESeq2] There is no difference in expression in my heatmap
DESeq2
heatmaps
2.9 years ago
Sooni
▴ 10
0
votes
1
reply
926
views
Extracting interaction contrast when using user supplied model.matrix
DESeq2
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
idetoma
• 0
1
vote
3
replies
1.4k
views
DESeq2 Installation Issue
DESeq2
updated 2.9 years ago by
Hervé Pagès
16k • written 2.9 years ago by
joanna
• 0
2
votes
4
replies
1.4k
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2
DifferentialExpression
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
idetoma
• 0
0
votes
1
reply
841
views
Rnaseq analysis using a continuous time series
DESeq2
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
Aviads
• 0
0
votes
2
replies
1.7k
views
installing DESeq2 on Macbook R Studio
DESeq2
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
Chatura
• 0
0
votes
1
reply
471
views
More information on results columns
DESeq2
updated 2.9 years ago by
ATpoint
★ 5.0k • written 2.9 years ago by
krigerkoalaen
• 0
0
votes
1
reply
879
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2
RNASeqData
DifferentialExpression
updated 2.9 years ago by
ATpoint
★ 5.0k • written 2.9 years ago by
Julie
• 0
1
vote
3
replies
3.7k
views
Do the count values should be only integer to be able to use DESeq2?
DESeq2
2.9 years ago
Sep
• 0
0
votes
5
replies
1.6k
views
Error running DESeq2 on longitudinal data: Error in checkFullRank(modelMatrix)
DESeq2
longitudinal
updated 2.9 years ago by
swbarnes2
★ 1.4k • written 2.9 years ago by
sharvari gujja
▴ 40
0
votes
1
reply
1.2k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 2.9 years ago by
Dario Strbenac
★ 1.6k • written 2.9 years ago by
Hicham
▴ 10
4
votes
7
replies
1.7k
views
DESeq2: Repetitive padj values?
DESeq2
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
vanbelj
▴ 30
1
vote
1
reply
1.0k
views
Is this DESeq2 interactions design correct?
DESeq2
interactions
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
bhagyesh
• 0
0
votes
3
replies
1.4k
views
how to iterate all comparisons in group with "coef =" ?
DESeq2
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
Theo
▴ 10
0
votes
1
reply
2.9k
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2
Transcriptomics
RNASeq
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
Jayesh Kumar
• 0
0
votes
1
reply
1.1k
views
Help for RNA sequencing analysis with DESEQ2
DESeq2
star
differentiallyexpressed
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
nico
• 0
1
vote
3
replies
1.5k
views
Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2
edgeR
rnaseqGene
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
vpl685
• 0
0
votes
1
reply
741
views
Combining VST counts for replicates
DESeq2
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
Jayesh Kumar
• 0
0
votes
1
reply
1.6k
views
How to set threshold of padj value in DeSeq2
DESeq2
padj
default
updated 2.9 years ago by
James W. MacDonald
68k • written 2.9 years ago by
Serena
• 0
0
votes
1
reply
766
views
Differential RNA seq on TCGA set
DESeq2
RNASeqData
updated 2.9 years ago by
ATpoint
★ 5.0k • written 2.9 years ago by
SilverCat
• 0
0
votes
1
reply
473
views
rlog() transformation works only when using DESeqDataSet, not matrix
DESeq2
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
licheny
• 0
0
votes
2
replies
770
views
Differential expression between samples of the same group
DESeq2
2.9 years ago
Oded
• 0
0
votes
1
reply
1.5k
views
Missing transcript
DESeq2
tximport
salmon
updated 2.9 years ago by
ATpoint
★ 5.0k • written 2.9 years ago by
camilia.savitri
• 0
1
vote
3
replies
1.7k
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
2.9 years ago
Alexandre
• 0
1
vote
4
replies
2.5k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
2.9 years ago
Iwan
• 0
0
votes
3
replies
1.3k
views
Differential gene expression analysis with data matrix generated with RSEM
DESeq2
edgeR
2.9 years ago
ubjw24
• 0
1
vote
1
reply
1.1k
views
Using the standard deviation of DESeq rlog transformed counts to identify genes for hierarchical clustering
DESeq2
updated 2.9 years ago by
ATpoint
★ 5.0k • written 2.9 years ago by
Josiah
• 0
1
vote
3
replies
9.3k
views
Manually calculating log2 fold change values from DESeq2 normalized counts
DESeq2
DifferentialExpression
2.9 years ago
Jayesh Kumar
• 0
0
votes
3
replies
1.4k
views
Tissue Level Differential Expression Analysis
DESeq2
DifferentialExpression
differentialex
Pseudobulk
SingleCell
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
skanda.hebbale
• 0
0
votes
4
replies
1.4k
views
suggest to report differential count estimate in DESeq2
DESeq2
2.9 years ago
Yongqing
• 0
2
votes
5
replies
2.7k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 21 months ago by
Michael Love
43k • written 2.9 years ago by
kiqbal
• 0
1
vote
6
replies
1.7k
views
low counts from microRNA seq
DESeq2
microRNA
HTSeq
2.9 years ago
abhay.kanodia
• 0
0
votes
2
replies
1.5k
views
DESeq2: overlap differentially expressed genes with and without interaction term
DESeq2
2.9 years ago
xuscha
• 0
1
vote
3
replies
4.1k
views
Error in SummarizedExperiment in DESeq2
DESeq2
3.0 years ago
Cherif
• 0
0
votes
3
replies
1.6k
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 2.9 years ago by
Michael Love
43k • written 3.0 years ago by
irish.prg
• 0
0
votes
1
reply
1.4k
views
DeSeq2 and GenomicRange installation possible conflict with bioconductor version 3.16?
DESeq2
version3.16
installation
bioconductor
GenomicRange
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
hong
• 0
1
vote
2
replies
2.2k
views
running DESeq2 from nanopore wf-alignment workflow
DESeq2
NanoporeRNASeq
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
shahla.kangachar
• 0
0
votes
2
replies
1.4k
views
Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR
DESeq2
updated 3.0 years ago by
chaco001
• 0 • written 3.4 years ago by
nc2849
• 0
0
votes
2
replies
1.3k
views
TnSeq as ZINB? Alternatives in R?
DESeq2
R
edgeR
Python
TnSeq
updated 3.0 years ago by
chaco001
• 0 • written 3.0 years ago by
David R
▴ 90
0
votes
3
replies
2.3k
views
Unusual MA and volcano plots?
DESeq2
RNASeq
written 3.0 years ago by
BT
▴ 10
0
votes
1
reply
676
views
How does DESeq2 handle multiple conditions in one design.
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
grsyhhsb
• 0
0
votes
1
reply
1.1k
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2
MultipleComparison
r
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
ncorak
• 0
0
votes
1
reply
912
views
Using DESeq2 for time-series analysis with two conditions
DESeq2
RNASeqData
updated 3.0 years ago by
ATpoint
★ 5.0k • written 3.0 years ago by
perceval.vellosillo
• 0
0
votes
1
reply
1.2k
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2
LRT
multifactorial
up/down-reg
log2FC
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
Laia
▴ 10
0
votes
2
replies
1.3k
views
Results analysis of differential gene expression using DESeq2 package
RnaSeqSampleSize
statistics
DESeq2
updated 3.0 years ago by
swbarnes2
★ 1.4k • written 3.0 years ago by
N
• 0
0
votes
2
replies
1.3k
views
How to filter for counts in different columns
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Konstantinos
• 0
0
votes
3
replies
1.5k
views
question about removing both known and unknown confounders
DESeq2
RUVSeq
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Lisa
• 0
0
votes
2
replies
862
views
checkFullRank(modelMatrix) while neither factor can be predicted from each other.
DESeq2
updated 3.0 years ago by
swbarnes2
★ 1.4k • written 3.0 years ago by
TzuChiao
▴ 10
1
vote
13
replies
3.0k
views
Deseq2 , result() taking too long > 3hrs
DESeq2
updated 2.8 years ago by
jon50250
• 0 • written 3.0 years ago by
Nidhi
• 0
4
votes
8
replies
3.5k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 2.5 years ago by
Gordon Smyth
53k • written 3.0 years ago by
Sabiha
▴ 20
4,840 results • Page
16 of 97
Recent ...
Replies
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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