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DeSeq2
•
reset
1
vote
2
replies
1.5k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2
BatchEffect
RNASeq
updated 3.1 years ago by
swbarnes2
★ 1.4k • written 3.1 years ago by
Flavio
• 0
0
votes
4
replies
1.1k
views
DESeq2 design with continuous variables AND filtering of low counts
DESeq2
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
bgurdon
• 0
2
votes
4
replies
1.7k
views
DiffBind and peak counts as input
DESeq2
edgeR
DiffBind
updated 3.0 years ago by
Rory Stark
★ 5.2k • written 3.1 years ago by
Bogdan
▴ 670
3
votes
12
replies
3.8k
views
t.test to determine the P-value in DESeq2
DESeq2
written 3.1 years ago by
Maryam.sed1400
• 0
2
votes
3
replies
2.6k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
updated 7 months ago by
ben
• 0 • written 3.1 years ago by
L
▴ 50
2
votes
2
replies
3.0k
views
Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed while using DESeq2
DESeq2
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
keremozdel9
• 0
0
votes
2
replies
2.4k
views
Cannot install bioconductor DESeq2 package on M1 mac ... any advice?
DESeq2
Install
r
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
Catherine
• 0
0
votes
8
replies
1.7k
views
disappearing of DEGs genes by adjusting P-value < 0.05
DESeq2
3.1 years ago
Maryam.sed1400
• 0
2
votes
2
replies
1.1k
views
Second covariate
DESeq2
3.1 years ago
liberios
▴ 10
1
vote
7
replies
1.7k
views
statistics : edger or DESeq2 to asses the differential binding using the average scores
DESeq2
edgeR
updated 3.0 years ago by
chaco001
• 0 • written 3.1 years ago by
Bogdan
▴ 670
0
votes
1
reply
1.1k
views
DESeq2 - Differential expression for miRNA data
DESeq2
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
Mariane
• 0
0
votes
2
replies
1.1k
views
Questions about `collapseReplicates` function in DESeq2
DESeq2
Transcriptomics
3.1 years ago
Yijing
• 0
0
votes
4
replies
1.9k
views
Skew of differentially expressed genes using DESeq2
DESeq2
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
b88dfe53
• 0
0
votes
2
replies
1.3k
views
How to do differential gene expression analysis of very highly sparsed single cell data?
DESeq2
3.1 years ago
Subhasis
• 0
0
votes
2
replies
1.9k
views
dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2
salmon
3.1 years ago
manduchi
▴ 10
0
votes
5
replies
1.5k
views
Running DESeq2 on viral infection without control/host data
DESeq2
viral
controls
3.1 years ago
f99942
• 0
0
votes
2
replies
1.2k
views
Unexpectedly low number of DE genes?
DESeq2
3.1 years ago
mhalache
• 0
0
votes
2
replies
911
views
RNA-seq DESeq2 factor design
DESeq2
3.1 years ago
Grace
• 0
0
votes
1
reply
4.3k
views
Heatmap with result DESeq analysis
DESeq2
results
Heatmaps
plots
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
Chiara
• 0
1
vote
20
replies
6.6k
views
Deseq2 installed, but there is no package called ‘Biostrings’
DESeq2
Install
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Hannah000111
• 0
0
votes
1
reply
2.5k
views
bigwig to counts
DESeq2
edgeR
bigwig
limma
3.1 years ago • updated 2.9 years ago
Bogdan
▴ 670
2
votes
5
replies
4.6k
views
DESeq2 with two continuous variable in a design
DESeq2
RNASeq
R
design
updated 3.1 years ago by
Michael Love
43k • written 4.4 years ago by
sofia
• 0
0
votes
1
reply
1.6k
views
I have problems installing DESeq2 using R4.1.2. It tells me that it is not available for my version of R and I need to upgrade my R version. but I ca…
DESeq2
updated 3.1 years ago by
shepherl
4.2k • written 3.1 years ago by
yari.hadi
• 0
0
votes
4
replies
1.5k
views
DESeq2 for ribo-IP analysis
DESeq2
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
Andy
• 0
3
votes
1
reply
1.4k
views
Identifying DEGs using lfcshrink()
DESeq2
lfcshrink
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
Zainab
▴ 20
0
votes
4
replies
1.4k
views
Is there a way to identify constituently expressed genes (not differentially expressed)?
DESeq2
3.1 years ago
nute11a
▴ 10
1
vote
2
replies
1.5k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2
scRNAseq
Fluidigm
3.2 years ago • updated 3.1 years ago
evocanres
• 0
3
votes
10
replies
3.1k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2
BatchEffect
fold
3.2 years ago • updated 3.1 years ago
eve.olszanowski
• 0
2
votes
1
reply
1.8k
views
Correcting for all the comparisons that have been made in analysis
DESeq2
comparisons
correction
updated 3.2 years ago by
James W. MacDonald
68k • written 3.2 years ago by
smac_head
• 0
3
votes
4
replies
1.9k
views
I have problems installing DESeq2 using R4.1.2. It tells me that it is not available for my version of R and I need to upgrade my R version. but I ca…
DESeq2
3.2 years ago
yari.hadi
• 0
1
vote
2
replies
1.2k
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2
BatchEffect
3.2 years ago
annamariabugaj
▴ 10
0
votes
3
replies
2.9k
views
Unable to load data "pasillaGenes" in R because DESeq is not installed?
DESeq2
pasillaGenes
updated 3.2 years ago by
James W. MacDonald
68k • written 4.9 years ago by
kanhasunny
• 0
0
votes
1
reply
2.0k
views
Does DeSeq2 make comparisons between all samples vs. all controls, or between matched samples and controls in different groups?
DESeq2
RNAseq
bulk
DifferentialExpression
updated 3.2 years ago by
James W. MacDonald
68k • written 3.2 years ago by
Maria
• 0
1
vote
1
reply
1.1k
views
Downloading DESeq package manually
DESeq2
Install
updated 3.2 years ago by
Basti
▴ 780 • written 3.2 years ago by
JAcky
• 0
1
vote
3
replies
9.2k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome
DESeq2
updated 3.2 years ago by
adR
▴ 40 • written 5.1 years ago by
Daniel
• 0
0
votes
1
reply
837
views
Extracting multi-design adjusted counts on DESeq2
DESeq2
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.2 years ago by
s26sw
• 0
0
votes
1
reply
1.1k
views
DIfferentially abundant taxa but some of them are not present in both groups (DESeq2)
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Valentín
• 0
0
votes
1
reply
982
views
DESEQ2 time series with multiple variables
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Abel
• 0
0
votes
1
reply
1.0k
views
Time serious analysis Wald test in results()
DESeq2
TimeSeriesExperiment
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Jason
• 0
3
votes
4
replies
2.9k
views
Comparing different method for DESEQ2
DESeq2
GeneExpression
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Vapin
• 0
0
votes
6
replies
2.9k
views
No differentially expressed genes after DESeq
DESeq2
R
3.2 years ago
Zach
• 0
3
votes
7
replies
2.9k
views
Different results between Limma and DESEQ2 for Differential Expression Analysis
DESeq2
limma
updated 3.2 years ago by
swbarnes2
★ 1.4k • written 3.2 years ago by
Bine
▴ 50
0
votes
4
replies
6.7k
views
Understanding the Log2FoldChange calculated with DESeq2 and according to formula log2(treated/control)
DESeq2
log2FC
3.2 years ago
User000
• 0
3
votes
5
replies
1.9k
views
DESEQ2 several samples per individual
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Bine
▴ 50
0
votes
1
reply
1.3k
views
Comparison between treatment timepoints in a single timeseries (control is first timepoint)
DESeq2
single-timeseries
TimeSeriesExperiment
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Jigyasa
• 0
0
votes
1
reply
1.2k
views
Set up "mock" cell type as the reference?
DESeq2
SingleCell
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Yiqi
▴ 10
1
vote
1
reply
923
views
Contrasts in Deseq2
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Pablo
• 0
0
votes
5
replies
3.2k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2
DEG
3.2 years ago • updated 3.1 years ago
marinaw
▴ 20
0
votes
1
reply
898
views
interaction term formula for DESEQ2?
DESeq2
updated 3.2 years ago by
swbarnes2
★ 1.4k • written 3.2 years ago by
barrypraveen
• 0
0
votes
1
reply
538
views
Bioconductor Rpackages install
DESeq2
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.2 years ago by
Imran
• 0
4,840 results • Page
18 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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