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Showing :
DESeq
•
reset
1
vote
2
replies
346
views
evaluate the variable importance on genes
DESeq2
deseq
12 weeks ago
Meme
• 0
0
votes
2
replies
350
views
Running DESeq on normalized data
deseq
DESeq2
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
Hugo
• 0
2
votes
2
replies
541
views
Predicting missing values splines DESeq2
deseq
DESeq2
6 months ago
georgii.vdovin
• 0
0
votes
1
reply
395
views
Controling for Covariates With a Continuous Predictor Variable
Deseq
DESeq2
updated 6 months ago by
Michael Love
42k • written 6 months ago by
georgii.vdovin
• 0
0
votes
1
reply
683
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
khaserdene99
• 0
0
votes
3
replies
980
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq
DESeq2
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
Abir.khazaal
▴ 10
0
votes
4
replies
673
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 10 months ago by
Michael Love
42k • written 10 months ago by
Ndimensional
▴ 20
1
vote
2
replies
634
views
summarizeToGene in tximeta causing vastly different results
DESeq2
deseq
txime
tximeta
updated 13 months ago by
Michael Love
42k • written 13 months ago by
akrunic
• 0
0
votes
4
replies
1.3k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 15 months ago by
Basti
▴ 780 • written 15 months ago by
Michael
• 0
0
votes
1
reply
576
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 15 months ago by
Michael Love
42k • written 15 months ago by
m-bihie
▴ 10
0
votes
1
reply
749
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 16 months ago by
Dario Strbenac
★ 1.5k • written 16 months ago by
Hicham
▴ 10
0
votes
2
replies
1.3k
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 12.3 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
1
vote
1
reply
533
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
barrypraveen
• 0
3
votes
2
replies
944
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
22 months ago
manwar
• 0
1
vote
1
reply
791
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 23 months ago by
Michael Love
42k • written 23 months ago by
stew
• 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq
RNASeqData
updated 23 months ago by
ATpoint
★ 4.1k • written 23 months ago by
Sanatan
• 0
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 2.0 years ago by
swbarnes2
★ 1.4k • written 2.0 years ago by
Hicham
▴ 10
1
vote
5
replies
1.5k
views
Potential outlier/high variance
deseq
DESeq2
updated 2.1 years ago by
Michael Love
42k • written 2.1 years ago by
Amali Thrimawithana
• 0
1
vote
2
replies
931
views
Deseq2 with imbalanced design
Deseq
2.2 years ago
Alex
• 0
1
vote
4
replies
1.6k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2
deseq
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
penny.lane
• 0
0
votes
2
replies
1.1k
views
DESeqDataSet design issue
DESeq
DESeq2
2.4 years ago
matthew.valentine
• 0
1
vote
1
reply
1.5k
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 2.6 years ago by
Michael Love
42k • written 2.6 years ago by
n.vandis
• 0
4
votes
6
replies
1.7k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
2.6 years ago
s-rhussien
• 0
2
votes
2
replies
2.3k
views
Correct way to make multiple comparisons on DESeq2?
DESeq
DESeq2
R
2.7 years ago
jbnrodriguez
▴ 10
1
vote
2
replies
998
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq
DESeq
2.7 years ago
krawczyk.margarita
• 0
0
votes
2
replies
1.5k
views
same padj for all the genes after DEseq analysis
etLRT
WALD
edgeR
DESEq
updated 2.8 years ago by
Michael Love
42k • written 2.8 years ago by
aiswaryabioinfo
• 0
0
votes
1
reply
1.1k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
3.0 years ago
ayy2110
• 0
1
vote
2
replies
960
views
metage problem with DESeq
DESeq
metagene2
metagene
updated 3.2 years ago by
ericfournier2
▴ 10 • written 3.2 years ago by
GM
▴ 10
0
votes
3
replies
2.3k
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 3.2 years ago by
Michael Love
42k • written 3.2 years ago by
sp
• 0
0
votes
5
replies
1.8k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2
ZINB
zinbwave
deseq
updated 3.3 years ago by
Michael Love
42k • written 3.3 years ago by
rowcyclecamp
• 0
2
votes
12
replies
4.5k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2
deseq
updated 3.6 years ago by
Michael Love
42k • written 9.0 years ago by
Nick
• 0
1
vote
2
replies
995
views
DESeq Error (nbinomTest ())
Deseq
nbinomTest
4.0 years ago
canfield
▴ 10
0
votes
7
replies
1.9k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
maniermk
• 0
2
votes
5
replies
5.7k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
written 4.1 years ago by
krunal.24.6
▴ 10
2
votes
2
replies
876
views
Mocking data for understanding interactions in DESeq2
deseq2
deseq
updated 4.1 years ago by
Simon Anders
★ 3.7k • written 4.1 years ago by
blawney
• 0
3
votes
5
replies
2.1k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq
rna-seq
filtering
DE
deseq2
updated 4.1 years ago by
Michael Love
42k • written 4.1 years ago by
svlachavas
▴ 830
1
vote
9
replies
1.3k
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 4.2 years ago by
Simon Anders
★ 3.7k • written 4.2 years ago by
megapode32559
• 0
0
votes
7
replies
1.2k
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2
deseq
4.3 years ago
MANYA_BIOINFO
• 0
0
votes
1
reply
1.3k
views
DESeq2 counts function not working
deseq2
Deseq
RNAseq
updated 4.5 years ago by
Michael Love
42k • written 4.5 years ago by
mrfossl97
▴ 10
2
votes
3
replies
1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 4.5 years ago by
Michael Love
42k • written 4.5 years ago by
Keith Hughitt
▴ 180
4
votes
4
replies
4.5k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 4.8 years ago by
wunderl
▴ 40 • written 4.8 years ago by
neekonsu
• 0
1
vote
2
replies
908
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 4.8 years ago by
Michael Love
42k • written 4.8 years ago by
sxv
• 0
0
votes
0
replies
958
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
4.9 years ago
kentfung
▴ 20
0
votes
9
replies
2.0k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
5.2 years ago
ariel
▴ 20
3
votes
12
replies
1.6k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
5.2 years ago
ariel
▴ 20
2
votes
3
replies
1.9k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
lefeverde
▴ 10
0
votes
1
reply
1.0k
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
FaisalH
• 0
0
votes
3
replies
1.2k
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2
rnaseq
rna-seq
deseq2
deseq
5.6 years ago
Ben
▴ 50
0
votes
7
replies
3.9k
views
DESeq2 install problem
deseq
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
bikashten
• 0
5
votes
7
replies
3.6k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
thindmarsmission
▴ 10
50 results • Page
1 of 1
Recent ...
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Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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