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Showing :
Deseq
•
reset
1
vote
2
replies
241
views
evaluate the variable importance on genes
DESeq2
deseq
5 weeks ago • updated 4 weeks ago
Meme
• 0
0
votes
2
replies
285
views
Running DESeq on normalized data
deseq
DESeq2
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
Hugo
• 0
2
votes
2
replies
472
views
Predicting missing values splines DESeq2
deseq
DESeq2
4 months ago
georgii.vdovin
• 0
0
votes
1
reply
341
views
Controling for Covariates With a Continuous Predictor Variable
Deseq
DESeq2
updated 4 months ago by
Michael Love
41k • written 4 months ago by
georgii.vdovin
• 0
0
votes
1
reply
588
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
khaserdene99
• 0
0
votes
3
replies
714
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq
DESeq2
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
Abir.khazaal
▴ 10
0
votes
4
replies
570
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 8 months ago by
Michael Love
41k • written 8 months ago by
Ndimensional
▴ 20
1
vote
2
replies
567
views
summarizeToGene in tximeta causing vastly different results
DESeq2
deseq
txime
tximeta
updated 11 months ago by
Michael Love
41k • written 11 months ago by
akrunic
• 0
0
votes
4
replies
1.1k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 13 months ago by
Basti
▴ 750 • written 13 months ago by
Michael
• 0
0
votes
1
reply
532
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 14 months ago by
Michael Love
41k • written 14 months ago by
m-bihie
▴ 10
0
votes
1
reply
662
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 14 months ago by
Dario Strbenac
★ 1.5k • written 14 months ago by
Hicham
▴ 10
0
votes
2
replies
1.2k
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 12.1 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
1
vote
1
reply
498
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 18 months ago by
ATpoint
★ 4.0k • written 18 months ago by
barrypraveen
• 0
3
votes
2
replies
879
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
20 months ago
manwar
• 0
1
vote
1
reply
746
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 21 months ago by
Michael Love
41k • written 21 months ago by
stew
• 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq
RNASeqData
updated 21 months ago by
ATpoint
★ 4.0k • written 21 months ago by
Sanatan
• 0
2
votes
1
reply
1.4k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 22 months ago by
swbarnes2
★ 1.3k • written 22 months ago by
Hicham
▴ 10
1
vote
5
replies
1.4k
views
Potential outlier/high variance
deseq
DESeq2
updated 23 months ago by
Michael Love
41k • written 23 months ago by
Amali Thrimawithana
• 0
1
vote
2
replies
858
views
Deseq2 with imbalanced design
Deseq
2.0 years ago
Alex
• 0
1
vote
4
replies
1.5k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2
deseq
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
penny.lane
• 0
0
votes
2
replies
1.0k
views
DESeqDataSet design issue
DESeq
DESeq2
2.3 years ago
matthew.valentine
• 0
1
vote
1
reply
1.4k
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
n.vandis
• 0
4
votes
6
replies
1.6k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
2.5 years ago
s-rhussien
• 0
2
votes
2
replies
2.2k
views
Correct way to make multiple comparisons on DESeq2?
DESeq
DESeq2
R
2.6 years ago • updated 2.5 years ago
jbnrodriguez
▴ 10
1
vote
2
replies
947
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq
DESeq
2.6 years ago
krawczyk.margarita
• 0
0
votes
2
replies
1.4k
views
same padj for all the genes after DEseq analysis
etLRT
WALD
edgeR
DESEq
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
aiswaryabioinfo
• 0
0
votes
1
reply
1.1k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
2.8 years ago
ayy2110
• 0
1
vote
2
replies
904
views
metage problem with DESeq
DESeq
metagene2
metagene
updated 3.0 years ago by
ericfournier2
▴ 10 • written 3.1 years ago by
GM
▴ 10
0
votes
3
replies
2.1k
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
sp
• 0
0
votes
5
replies
1.6k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2
ZINB
zinbwave
deseq
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
rowcyclecamp
• 0
2
votes
12
replies
4.4k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2
deseq
updated 3.4 years ago by
Michael Love
41k • written 8.9 years ago by
Nick
• 0
1
vote
2
replies
954
views
DESeq Error (nbinomTest ())
Deseq
nbinomTest
3.8 years ago
canfield
▴ 10
0
votes
7
replies
1.7k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
maniermk
• 0
2
votes
5
replies
5.3k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
written 4.0 years ago by
krunal.24.6
▴ 10
2
votes
2
replies
823
views
Mocking data for understanding interactions in DESeq2
deseq2
deseq
updated 4.0 years ago by
Simon Anders
★ 3.7k • written 4.0 years ago by
blawney
• 0
3
votes
5
replies
2.0k
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 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
svlachavas
▴ 830
1
vote
9
replies
1.2k
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 4.0 years ago by
Simon Anders
★ 3.7k • written 4.0 years ago by
megapode32559
• 0
0
votes
7
replies
1.1k
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2
deseq
4.2 years ago
MANYA_BIOINFO
• 0
0
votes
1
reply
1.2k
views
DESeq2 counts function not working
deseq2
Deseq
RNAseq
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
mrfossl97
▴ 10
2
votes
3
replies
1.3k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
Keith Hughitt
▴ 180
4
votes
4
replies
4.4k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 4.6 years ago by
wunderl
▴ 40 • written 4.7 years ago by
neekonsu
• 0
1
vote
2
replies
850
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
sxv
• 0
0
votes
0
replies
909
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
4.7 years ago
kentfung
▴ 20
0
votes
9
replies
1.9k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
5.1 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
5.1 years ago
ariel
▴ 20
2
votes
3
replies
1.8k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
lefeverde
▴ 10
0
votes
1
reply
994
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
FaisalH
• 0
0
votes
3
replies
1.1k
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2
rnaseq
rna-seq
deseq2
deseq
5.5 years ago
Ben
▴ 50
0
votes
7
replies
3.9k
views
DESeq2 install problem
deseq
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
bikashten
• 0
5
votes
7
replies
3.5k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
thindmarsmission
▴ 10
50 results • Page
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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