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DESeq2
•
reset
51
votes
20
replies
35k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 6.7 years ago by
adam
• 0 • written 7.1 years ago by
AB
▴ 110
32
votes
21
replies
11k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
8.4 years ago • updated 4 months ago
Michael Love
39k
30
votes
16
replies
14k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 4.8 years ago by
luxeredias
▴ 20 • written 6.6 years ago by
tangming2005
▴ 190
25
votes
11
replies
6.7k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq
deseq2
edgeR
normalization
updated 7.2 years ago by
Simon Anders
★ 3.7k • written 7.2 years ago by
Nik Tuzov
▴ 80
24
votes
7
replies
12k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq
deseq2
ercc
updated 6.3 years ago by
Simon Anders
★ 3.7k • written 6.3 years ago by
mbeckste
▴ 30
24
votes
6
replies
29k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2
r
updated 10 months ago by
Hongwei
▴ 20 • written 6.1 years ago by
tombernardryan
▴ 50
24
votes
22
replies
15k
views
DESeq2 for ChIP-seq differential peaks
deseq2
deseq
chipseq
updated 5.6 years ago by
k.vitting.seerup
▴ 120 • written 7.4 years ago by
tangming2005
▴ 190
23
votes
6
replies
7.3k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2
rnaseq
statistics
updated 5.3 years ago by
James W. MacDonald
62k • written 5.3 years ago by
Russ Fraser
▴ 30
23
votes
14
replies
36k
views
deseq2 filter the low counts
deseq2
lowcount
updated 23 months ago by
Michael Love
39k • written 7.9 years ago by
aristotele_m
▴ 30
21
votes
12
replies
20k
views
New function lfcShrink() in DESeq2
deseq2
updated 3.5 years ago by
Micheal Stark
• 0 • written 5.8 years ago by
Michael Love
39k
21
votes
17
replies
5.2k
views
DESeq2 1.20.0 lfcshrink function
deseq2
differential expression
logfoldchange
lfcshrink
lfcthreshold
updated 20 months ago by
Michael Love
39k • written 4.6 years ago by
emi.sch
▴ 20
21
votes
7
replies
6.5k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma
deseq2
edger
rnaseq
updated 5.4 years ago by
Gordon Smyth
47k • written 5.4 years ago by
Jack
• 0
18
votes
12
replies
2.8k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR
deseq2
rna-seq
independent filtering
updated 7.6 years ago by
Michael Love
39k • written 7.6 years ago by
Ryan C. Thompson
7.8k
18
votes
4
replies
27k
views
FDR and padj in deseq and edger
deseq2
edger
updated 7.3 years ago by
Gordon Smyth
47k • written 7.3 years ago by
tonja.r
▴ 80
18
votes
24
replies
12k
views
[DESeq2] time series strain-specific differences over time
deseq2
timecourse
updated 24 months ago by
ethicalhackers
• 0 • written 7.9 years ago by
john
▴ 120
16
votes
9
replies
24k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 2.0 years ago by
Michael Love
39k • written 7.0 years ago by
ribioinfo
▴ 100
16
votes
7
replies
8.9k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2
ensembl
updated 5.0 years ago by
James W. MacDonald
62k • written 5.0 years ago by
casey.rimland
▴ 150
16
votes
7
replies
9.9k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2
lfc
coef
contrast
updated 5.5 years ago by
Michael Love
39k • written 5.5 years ago by
Anke Busch
▴ 10
16
votes
40
replies
5.0k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 13 months ago by
Clara
• 0 • written 3.5 years ago by
lim6432
▴ 50
16
votes
9
replies
5.0k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 5.3 years ago by
Rory Stark
★ 4.6k • written 6.9 years ago by
florian.noack
▴ 60
15
votes
7
replies
4.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 6.7 years ago by
Ryan C. Thompson
7.8k • written 6.7 years ago by
ompandey
▴ 10
15
votes
12
replies
1.9k
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 4.5 years ago by
Michael Love
39k • written 4.5 years ago by
rory.kirchner
▴ 60
15
votes
18
replies
1.2k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2
edgeR
goana
GO
updated 10 months ago by
Gordon Smyth
47k • written 10 months ago by
Raito92
▴ 60
15
votes
8
replies
10k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2
deseq
8.2 years ago
salahm
▴ 70
15
votes
4
replies
2.0k
views
Using multiple tools for differential gene expression analysis as validation
edger
limma
deseq2
rnaseq
updated 6.6 years ago by
Ryan C. Thompson
7.8k • written 6.6 years ago by
WouterDeCoster
▴ 130
15
votes
12
replies
53k
views
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 7.9 years ago by
Steve Lianoglou
13k • written 7.9 years ago by
john
▴ 120
14
votes
19
replies
8.0k
views
DESeq2 Model Design
DESeq2
linear model
model
updated 21 months ago by
Michael Love
39k • written 8.2 years ago by
andrew.j.skelton73
▴ 360
14
votes
9
replies
12k
views
How does DESeq2 handle zero counts in one condition?
deseq2
deseq
rna-seq
8.1 years ago
gavrielmatt
▴ 30
14
votes
15
replies
46k
views
DESeq2 output explanation
deseq
deseq2
updated 15 months ago by
Michael Love
39k • written 8.2 years ago by
francesca.defilippis
▴ 80
14
votes
19
replies
16k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2
annotation
granges
updated 12 months ago by
Nadine
▴ 50 • written 8.3 years ago by
Darya Vanichkina
▴ 120
13
votes
5
replies
31k
views
plotPCA - how to add labels to a PCA plot
plotPCA
deseq2
labels
updated 6.1 years ago by
Federico Marini
▴ 150 • written 6.1 years ago by
al-ash
▴ 50
13
votes
6
replies
6.1k
views
DESeq2 multiple interaction terms 3-factor design
deseq2
deseq
interactions
multiple factor design
updated 7.1 years ago by
Michael Love
39k • written 7.1 years ago by
Stephen Turner
▴ 290
13
votes
10
replies
3.2k
views
Big differences in logfoldchange for some genes between edgeR and DESeq2
edger
deseq2
updated 7.2 years ago by
Gordon Smyth
47k • written 7.2 years ago by
Matarit
• 0
13
votes
4
replies
17k
views
Dealing with genes that have Padj=NA
deseq2
updated 4.5 years ago by
Fuqi Xu
▴ 10 • written 7.1 years ago by
raya.fai
▴ 60
13
votes
16
replies
3.9k
views
Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR
deseq2
ase
allele
7.3 years ago
trianglescout
▴ 40
12
votes
1
reply
5.7k
views
identifying the samples on plotPCA
deseq2
plotpca
PCa
updated 5.3 years ago by
Michael Love
39k • written 5.3 years ago by
lirongrossmann
▴ 70
12
votes
4
replies
18k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 2.5 years ago by
Ram
▴ 160 • written 2.5 years ago by
c.e.chong
▴ 10
12
votes
6
replies
19k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2
multiple factor design
updated 7.7 years ago by
Michael Love
39k • written 7.7 years ago by
kmu004
▴ 50
12
votes
11
replies
3.2k
views
Memory usage for bplapply -- is the entire environment copied over to each worker thread?
bplapply
biocparallel
deseq2
updated 7.6 years ago by
Valerie Obenchain
★ 6.7k • written 7.6 years ago by
Lauren
▴ 40
12
votes
8
replies
1.3k
views
DESeq fitted values using coefficients vs mu
deseq2
updated 6.1 years ago by
Michael Love
39k • written 6.1 years ago by
Matthew McCall
▴ 830
12
votes
6
replies
2.6k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq
deseq2
edger
7.2 years ago
martiningi
▴ 40
11
votes
10
replies
2.8k
views
Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a transcriptome?
deseq2
nanopore
3.8 years ago
David Eccles (gringer)
▴ 30
11
votes
7
replies
13k
views
DESeq2: multiple conditions design -- How to select subset comparisons from the DESeq object for PCA, ...
deseq2
updated 15 months ago by
Michael Love
39k • written 6.9 years ago by
martin.hoelzer
▴ 20
11
votes
8
replies
7.1k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA
RNA-Seq
DESeq2
voom
removebatcheffect()
updated 6.4 years ago by
Peter Langfelder
★ 2.7k • written 6.4 years ago by
gokce.ouz
▴ 70
11
votes
4
replies
30k
views
DESeq2 baseMean counts
deseq2
updated 7.2 years ago by
Michael Love
39k • written 7.2 years ago by
zpingfeng
• 0
11
votes
14
replies
8.6k
views
Is there a conceptual difference between vst/rlog transforms and lfcShrink?
deseq2
updated 5.1 years ago by
Michael Love
39k • written 5.1 years ago by
kieran.mace
▴ 40
11
votes
3
replies
694
views
lfcShrink function for different comparison
DESeq2
RNASeq
updated 12 months ago by
molly_the_minotaur
▴ 30 • written 2.2 years ago by
bi.mi
▴ 60
10
votes
6
replies
3.7k
views
Log2FoldChange shrinkage method in DESeq2
deseq2
apeglm
lfcshrink
updated 4.7 years ago by
Michael Love
39k • written 4.7 years ago by
Benjamin Ostendorf
▴ 90
10
votes
9
replies
9.1k
views
DESeq2 baseMean values for each sample
deseq2
8.2 years ago
aburkha69
▴ 30
10
votes
1
reply
13k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq
deseq2
updated 7.2 years ago by
Michael Love
39k • written 7.2 years ago by
tony_cybercloud
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
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…
Comment: Question about GWASTools gdsSubset
by
Stephanie M. Gogarten
▴ 840
You could see if an attribute has been set on the genotype node indicating the order: ``` > library(gdsfmt) > gdsfile <- system.file("extda…
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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