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DESeq2
•
reset
52
votes
20
replies
50k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 8.9 years ago by
adam
• 0 • written 9.4 years ago by
AB
▴ 110
38
votes
23
replies
17k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
10.6 years ago • updated 5 weeks ago
Michael Love
43k
34
votes
29
replies
16k
views
[DESeq2] time series strain-specific differences over time
deseq2
timecourse
updated 7 months ago by
Michael Love
43k • written 10.1 years ago by
john
▴ 130
32
votes
16
replies
20k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 7.0 years ago by
luxeredias
▴ 20 • written 8.8 years ago by
tangming2005
▴ 200
30
votes
21
replies
59k
views
deseq2 filter the low counts
deseq2
lowcount
updated 15 months ago by
Xiao
• 0 • written 10.2 years ago by
aristotele_m
▴ 40
28
votes
6
replies
45k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2
r
updated 3.1 years ago by
Hongwei
▴ 20 • written 8.3 years ago by
tombernardryan
▴ 60
28
votes
7
replies
13k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2
rnaseq
statistics
updated 19 months ago by
camillab.
▴ 10 • written 7.5 years ago by
Russ Fraser
▴ 40
27
votes
17
replies
9.1k
views
DESeq2 1.20.0 lfcshrink function
deseq2
differential expression
logfoldchange
lfcshrink
lfcthreshold
updated 3.9 years ago by
Michael Love
43k • written 6.8 years ago by
emi.sch
▴ 50
27
votes
7
replies
16k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq
deseq2
ercc
updated 8.5 years ago by
Simon Anders
★ 3.8k • written 8.5 years ago by
mbeckste
▴ 30
27
votes
22
replies
22k
views
DESeq2 for ChIP-seq differential peaks
deseq2
deseq
chipseq
updated 7.8 years ago by
k.vitting.seerup
▴ 120 • written 9.6 years ago by
tangming2005
▴ 200
25
votes
7
replies
12k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma
deseq2
edger
rnaseq
updated 7.6 years ago by
Gordon Smyth
52k • written 7.6 years ago by
Jack
▴ 20
25
votes
11
replies
8.7k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq
deseq2
edgeR
normalization
updated 9.4 years ago by
Simon Anders
★ 3.8k • written 9.4 years ago by
Nik Tuzov
▴ 90
22
votes
12
replies
29k
views
New function lfcShrink() in DESeq2
deseq2
updated 5.7 years ago by
Micheal Stark
• 0 • written 8.0 years ago by
Michael Love
43k
20
votes
15
replies
67k
views
DESeq2 output explanation
deseq
deseq2
updated 3.5 years ago by
Michael Love
43k • written 10.5 years ago by
francesca.defilippis
▴ 100
19
votes
7
replies
14k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2
ensembl
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
casey.rimland
▴ 170
18
votes
12
replies
4.4k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR
deseq2
rna-seq
independent filtering
updated 9.9 years ago by
Michael Love
43k • written 9.9 years ago by
Ryan C. Thompson
★ 7.9k
18
votes
4
replies
41k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 4.7 years ago by
Ram
▴ 220 • written 4.7 years ago by
c.e.chong
▴ 10
18
votes
4
replies
37k
views
FDR and padj in deseq and edger
deseq2
edger
updated 9.5 years ago by
Gordon Smyth
52k • written 9.5 years ago by
tonja.r
▴ 80
17
votes
11
replies
40k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 10 months ago by
Michael Love
43k • written 9.3 years ago by
ribioinfo
▴ 100
17
votes
7
replies
15k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2
lfc
coef
contrast
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
Anke Busch
▴ 10
17
votes
13
replies
21k
views
deseq2 normalized data with heatmap
deseq2
updated 3.8 years ago by
Ian
▴ 10 • written 4.7 years ago by
linouhao
▴ 20
17
votes
9
replies
7.6k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 7 months ago by
James W. MacDonald
68k • written 8.9 years ago by
ompandey
▴ 10
16
votes
40
replies
11k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 3.3 years ago by
Clara
▴ 10 • written 5.8 years ago by
lim6432
▴ 50
16
votes
12
replies
3.4k
views
VST transformation (DESeq2) for metabolomics data
vst
Metabolomics
DESeq2
3.0 years ago
Joan Miró
▴ 80
16
votes
19
replies
21k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2
annotation
granges
updated 3.2 years ago by
Nadine
▴ 60 • written 10.5 years ago by
Darya Vanichkina
▴ 130
16
votes
12
replies
8.6k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 7 months ago by
khanwaled68
• 0 • written 9.1 years ago by
florian.noack
▴ 60
15
votes
12
replies
3.1k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2
ZINB-WaVE
single cell
RNA-seq
differential expression
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
rory.kirchner
▴ 60
15
votes
18
replies
4.6k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2
edgeR
goana
GO
updated 3.1 years ago by
Gordon Smyth
52k • written 3.1 years ago by
Raito92
▴ 60
15
votes
3
replies
2.2k
views
lfcShrink function for different comparison
DESeq2
RNASeq
updated 3.2 years ago by
molly_the_minotaur
▴ 30 • written 4.5 years ago by
bi.mi
▴ 90
15
votes
12
replies
76k
views
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 10.1 years ago by
Steve Lianoglou
★ 13k • written 10.1 years ago by
john
▴ 130
15
votes
8
replies
12k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2
deseq
10.5 years ago • updated 10.4 years ago
salahm
▴ 70
15
votes
4
replies
3.5k
views
Using multiple tools for differential gene expression analysis as validation
edger
limma
deseq2
rnaseq
updated 8.8 years ago by
Ryan C. Thompson
★ 7.9k • written 8.8 years ago by
WouterDeCoster
▴ 130
14
votes
19
replies
9.8k
views
DESeq2 Model Design
DESeq2
linear model
model
updated 4.0 years ago by
Michael Love
43k • written 10.4 years ago by
andrew.j.skelton73
▴ 370
14
votes
5
replies
24k
views
Dealing with genes that have Padj=NA
deseq2
updated 21 months ago by
Juan Pablo
• 0 • written 9.4 years ago by
raya.fai
▴ 60
14
votes
22
replies
32k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 14 months ago by
Michael Love
43k • written 8.8 years ago by
adesrichard
▴ 30
14
votes
9
replies
17k
views
How does DESeq2 handle zero counts in one condition?
deseq2
deseq
rna-seq
10.3 years ago
gavrielmatt
▴ 30
14
votes
5
replies
48k
views
plotPCA - how to add labels to a PCA plot
plotPCA
deseq2
labels
updated 8.3 years ago by
Federico Marini
▴ 180 • written 8.3 years ago by
al-ash
▴ 50
13
votes
16
replies
6.1k
views
Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR
deseq2
ase
allele
9.5 years ago
trianglescout
▴ 40
13
votes
6
replies
7.7k
views
DESeq2 multiple interaction terms 3-factor design
deseq2
deseq
interactions
multiple factor design
updated 9.3 years ago by
Michael Love
43k • written 9.3 years ago by
Stephen Turner
▴ 290
13
votes
10
replies
4.5k
views
Big differences in logfoldchange for some genes between edgeR and DESeq2
edger
deseq2
updated 9.4 years ago by
Gordon Smyth
52k • written 9.4 years ago by
Matarit
• 0
12
votes
9
replies
12k
views
DESeq2 baseMean values for each sample
deseq2
10.4 years ago
aburkha69
▴ 30
12
votes
4
replies
4.8k
views
WGCNA following salmon/DESeq2
deseq2
wgcna
salmon
updated 6.4 years ago by
Peter Langfelder
★ 3.0k • written 6.4 years ago by
maya.kappil
▴ 30
12
votes
6
replies
22k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2
multiple factor design
updated 10.0 years ago by
Michael Love
43k • written 10.0 years ago by
kmu004
▴ 50
12
votes
1
reply
8.2k
views
identifying the samples on plotPCA
deseq2
plotpca
PCa
updated 7.5 years ago by
Michael Love
43k • written 7.5 years ago by
lirongrossmann
▴ 80
12
votes
14
replies
35k
views
DESeq2 normalization vs VST vs rlog
deseq2
updated 2.4 years ago by
Jiahua
• 0 • written 5.7 years ago by
Jonas B.
▴ 40
12
votes
11
replies
5.0k
views
Memory usage for bplapply -- is the entire environment copied over to each worker thread?
bplapply
biocparallel
deseq2
updated 9.8 years ago by
Valerie Obenchain
★ 6.8k • written 9.8 years ago by
Lauren
▴ 40
12
votes
6
replies
3.9k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq
deseq2
edger
9.4 years ago
martiningi
▴ 40
12
votes
8
replies
2.5k
views
DESeq fitted values using coefficients vs mu
deseq2
updated 8.3 years ago by
Michael Love
43k • written 8.3 years ago by
Matthew McCall
▴ 830
12
votes
18
replies
6.8k
views
What is the correct use of removeBatchEffect's design parameter
deseq2
limma
updated 4.1 years ago by
Gordon Smyth
52k • written 4.6 years ago by
Sam
▴ 10
11
votes
8
replies
11k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA
RNA-Seq
DESeq2
voom
removebatcheffect()
updated 8.6 years ago by
Peter Langfelder
★ 3.0k • written 8.6 years ago by
gokce.ouz
▴ 70
50 results • Page
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Comment: Bioconductor 3.20 Release Schedule
by
randyprice13102000
• 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq
by
ATpoint
★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2
by
ATpoint
★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness
by
ATpoint
★ 4.8k
> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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