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DESEQ2
•
reset
0
votes
2
replies
2.6k
views
Issues installing packages miniconda environment
bioclite
deseq2
miniconda
packages
7.7 years ago
cpat
• 0
1
vote
12
replies
2.2k
views
DESeq2 multifactor design with interaction term
deseq2
multiple factor design
interaction term
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
Giovanni Bacci
• 0
4
votes
12
replies
2.6k
views
Incredibly high/low foldChange
deseq2
7.7 years ago
jovel_juan
▴ 30
2
votes
3
replies
2.1k
views
RNA-seq: Time-course data normalisation with TPM
rna-seq
normalization
deseq2
TPM
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
heikki.sarin
▴ 10
1
vote
2
replies
1.3k
views
Interpretation of results names after LRT
DESeq2
LRT
multiple time points
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
A
▴ 60
0
votes
5
replies
1.8k
views
results {DESeq2} parameters
deseq2
results
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
Aurora
▴ 20
0
votes
1
reply
1.2k
views
Removal of outliers after library size correction, can I save this to my dds object?
deseq2
outliers
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
Moose123
• 0
1
vote
1
reply
1.9k
views
DESeq2 question about predicting abundance adjusted for covariates.
deseq2
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
migimimi0
• 0
0
votes
3
replies
2.3k
views
choose between normalization techniques for OTU counts
deseq2
normalization
R
edger
7.7 years ago
apfelbapfel
▴ 30
0
votes
6
replies
2.2k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2
design
interaction term
R
written 7.7 years ago by
briverog
• 0
1
vote
2
replies
3.3k
views
use tximport's countsFromAbundance when using DESeq2
deseq2
tximport
normalization
salmon
rnaseq
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
ginlucks
• 0
7
votes
4
replies
4.0k
views
Normalized counts of DESeq2 affected by design formula?
deseq2
updated 22 months ago by
Garrett
• 0 • written 7.7 years ago by
blastzone.heimerdinger
▴ 20
0
votes
1
reply
1.6k
views
Best way to analyze multiple treatments using DESeq2?
deseq2
rna-seq
mirna
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
michael.frech
• 0
1
vote
1
reply
1.6k
views
DESeq, DESeq2 or EdgeR normalization for gene expression on multiple tissues without replicates ?
normalization
deseq2
edger
updated 7.7 years ago by
Aaron Lun
★ 29k • written 7.7 years ago by
giulia.pasquesi
▴ 10
2
votes
2
replies
1.2k
views
Does "FRY gene set tests" is possible using a DESEQ2 style analysis ?
deseq2
fry gene tests
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
Aurora
▴ 20
0
votes
6
replies
2.1k
views
weird behaviour DESeq2 1.18.1
deseq2
outliers
version
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
aec
▴ 90
1
vote
3
replies
1.5k
views
plotMA (DESeq2) Issue
deseq2
plotMA
rnaseq
logfoldchange
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
ap_vc21
• 0
0
votes
1
reply
649
views
Does DeSeq2 normalizes for high sample variance between biological replicates?
deseq2
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
gupta
• 0
4
votes
4
replies
3.2k
views
Using DADA2 output for DESeq2
deseq2
dada2
updated 7.7 years ago by
benjamin.j.callahan
▴ 50 • written 7.7 years ago by
blastzone.heimerdinger
▴ 20
0
votes
1
reply
1.3k
views
Changing group labels yields different results in DESeq2
deseq2
multiple groups
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
blobbyscience
• 0
1
vote
3
replies
1.0k
views
very low number in normalized count but give very high in log2foldchange
deseq2
7.7 years ago
naktang1
• 0
0
votes
3
replies
2.1k
views
Error in DESeq "object" not found
deseq2
LRT
reduced model
updated 7.7 years ago by
James W. MacDonald
68k • written 7.7 years ago by
A
▴ 60
8
votes
2
replies
11k
views
DESeq2 analysis with only two replicates
deseq2
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
jovel_juan
▴ 30
0
votes
11
replies
2.8k
views
Strange dispersion plot
deseq2
dispersion
7.7 years ago
Moose123
• 0
0
votes
4
replies
3.8k
views
DESeq2 - DESeqDatasetFromMatrix
deseq2
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
csijst
• 0
0
votes
2
replies
971
views
Re-calculate DESeq from dds based on another design
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
Raymond
▴ 20
0
votes
2
replies
939
views
find gene only express in one condition in Deseq2
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
naktang1
• 0
1
vote
5
replies
2.3k
views
To analyze the overall variance, which one to choose, vst or DESeq2 normalized counts?
deseq2
updated 7.8 years ago by
Alan
▴ 20 • written 7.8 years ago by
Raymond
▴ 20
1
vote
2
replies
2.7k
views
DESeq2 - MAP and MLE - log2FoldChange
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
thomasjenner333
• 0
0
votes
1
reply
532
views
DESeq2 package - different results
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
meshi.barsheshet
• 0
2
votes
1
reply
1.1k
views
DESeq2-No replicates-Utility of log2fold shrunk values?
deseq2
rnaseq
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
bn3301
• 0
1
vote
8
replies
2.1k
views
design versus interaction term similarities and/or differences?
deseq2
ANOVA
design
interaction term
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
tarun2
• 0
1
vote
2
replies
2.1k
views
lfcShrink: Error when using numerical contrast vector
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
amalthomas111
• 0
2
votes
1
reply
5.5k
views
Using DESeq2 to analyse TCGA data
deseq2
tcga
tcgabiolinks
gene expression
differential expression
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
victor.ramos.usp
• 0
0
votes
8
replies
6.6k
views
Comparing between two differential expression analysis - two different fold changes
Deseq
deseq2
differential gene expression
rnaseq
statistical test
7.8 years ago
Marina
▴ 40
3
votes
5
replies
2.0k
views
How to set up the Wald test testing for log2 fold change above a threshold, and interpret the result correctly?
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
Alan
▴ 20
3
votes
16
replies
3.1k
views
DESeq2 interaction term
DESeq2
7.8 years ago
Catalina Aguilar Hurtado
▴ 90
0
votes
5
replies
1.1k
views
Different version of DESeq2
deseq2
mikelove
7.8 years ago
marika.catapano
• 0
6
votes
7
replies
6.4k
views
Is it reasonable to run DESeq2 on only a subset of transcripts of the original raw count matrix?
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
Alan
▴ 20
3
votes
4
replies
2.0k
views
DESeq2 for Time course experiments
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
hwu12
▴ 10
0
votes
10
replies
1.6k
views
DESEQ2 Grouping vs interaction and dds
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
aangajala
▴ 20
0
votes
2
replies
4.5k
views
DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2
goseq
rnaseq
go enrichment
differential gene expression
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
josef.oeckl
• 0
0
votes
2
replies
1.7k
views
Filtering genes with a minimum number of counts between samples
DESeq2
filtering
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
A
▴ 60
0
votes
4
replies
1.1k
views
Using a truth table for ColumnData in DESeq2
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
jrlarsen
▴ 10
0
votes
4
replies
1.8k
views
Normalise counts when tumour samples have normal tissue contamination.
deseq2
deseq
edgeR
rnaseq
htseqcounts
7.8 years ago
Deepali
• 0
0
votes
2
replies
2.7k
views
Deseq2 raw counts input as integers
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
Catalina Aguilar Hurtado
▴ 90
1
vote
2
replies
3.3k
views
DESeq2 plotCounts() function-what is the unit on y axis?
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
Alan
▴ 20
2
votes
3
replies
1.2k
views
DESeq2 using multiple conditions
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
aangajala
▴ 20
0
votes
4
replies
2.4k
views
Deseq2 padj value very low
deseq2
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
jarod_v6@libero.it
▴ 40
3
votes
8
replies
2.0k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT
CPM
lowcountgenes
deseq2
7.8 years ago
A
▴ 60
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