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Deseq
•
reset
1
vote
2
replies
392
views
evaluate the variable importance on genes
DESeq2
deseq
4 months ago
Meme
• 0
0
votes
2
replies
394
views
Running DESeq on normalized data
deseq
DESeq2
updated 6 months ago by
ATpoint
★ 4.2k • written 6 months ago by
Hugo
• 0
2
votes
2
replies
590
views
Predicting missing values splines DESeq2
deseq
DESeq2
7 months ago
georgii.vdovin
• 0
0
votes
1
reply
430
views
Controling for Covariates With a Continuous Predictor Variable
Deseq
DESeq2
updated 8 months ago by
Michael Love
42k • written 8 months ago by
georgii.vdovin
• 0
0
votes
1
reply
758
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 9 months ago by
James W. MacDonald
66k • written 9 months ago by
khaserdene99
• 0
0
votes
3
replies
1.2k
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq
DESeq2
updated 11 months ago by
ATpoint
★ 4.2k • written 11 months ago by
Abir.khazaal
▴ 10
0
votes
4
replies
739
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 11 months ago by
Michael Love
42k • written 11 months ago by
Ndimensional
▴ 20
1
vote
2
replies
683
views
summarizeToGene in tximeta causing vastly different results
DESeq2
deseq
txime
tximeta
updated 14 months ago by
Michael Love
42k • written 14 months ago by
akrunic
• 0
0
votes
4
replies
1.4k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 16 months ago by
Basti
▴ 780 • written 16 months ago by
Michael
• 0
0
votes
1
reply
604
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 17 months ago by
Michael Love
42k • written 17 months ago by
m-bihie
▴ 10
0
votes
1
reply
810
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 17 months ago by
Dario Strbenac
★ 1.5k • written 17 months ago by
Hicham
▴ 10
0
votes
2
replies
1.3k
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 12.4 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
1
vote
1
reply
555
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 22 months ago by
ATpoint
★ 4.2k • written 22 months ago by
barrypraveen
• 0
3
votes
2
replies
993
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
23 months ago
manwar
• 0
1
vote
1
reply
830
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 2.1 years ago by
Michael Love
42k • written 2.1 years ago by
stew
• 0
1
vote
5
replies
1.3k
views
Error in DEseq
DEseq
RNASeqData
updated 2.1 years ago by
ATpoint
★ 4.2k • written 2.1 years ago by
Sanatan
• 0
2
votes
1
reply
1.6k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 2.1 years ago by
swbarnes2
★ 1.4k • written 2.1 years ago by
Hicham
▴ 10
1
vote
5
replies
1.5k
views
Potential outlier/high variance
deseq
DESeq2
updated 2.2 years ago by
Michael Love
42k • written 2.2 years ago by
Amali Thrimawithana
• 0
1
vote
2
replies
963
views
Deseq2 with imbalanced design
Deseq
2.3 years ago
Alex
• 0
1
vote
4
replies
1.7k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2
deseq
updated 2.4 years ago by
Michael Love
42k • written 2.4 years ago by
penny.lane
• 0
0
votes
2
replies
1.1k
views
DESeqDataSet design issue
DESeq
DESeq2
2.6 years ago
matthew.valentine
• 0
1
vote
1
reply
1.6k
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 2.7 years ago by
Michael Love
42k • written 2.7 years ago by
n.vandis
• 0
4
votes
6
replies
1.8k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
2.8 years ago
s-rhussien
• 0
2
votes
2
replies
2.4k
views
Correct way to make multiple comparisons on DESeq2?
DESeq
DESeq2
R
2.8 years ago
jbnrodriguez
▴ 10
1
vote
2
replies
1.0k
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq
DESeq
2.9 years ago
krawczyk.margarita
• 0
0
votes
2
replies
1.6k
views
same padj for all the genes after DEseq analysis
etLRT
WALD
edgeR
DESEq
updated 2.9 years ago by
Michael Love
42k • written 2.9 years ago by
aiswaryabioinfo
• 0
0
votes
1
reply
1.2k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
3.1 years ago
ayy2110
• 0
1
vote
2
replies
1.0k
views
metage problem with DESeq
DESeq
metagene2
metagene
updated 3.3 years ago by
ericfournier2
▴ 10 • written 3.3 years ago by
GM
▴ 10
0
votes
3
replies
2.5k
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 3.3 years ago by
Michael Love
42k • written 3.3 years ago by
sp
• 0
0
votes
5
replies
1.9k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2
ZINB
zinbwave
deseq
updated 3.4 years ago by
Michael Love
42k • written 3.4 years ago by
rowcyclecamp
• 0
2
votes
12
replies
4.6k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2
deseq
updated 3.7 years ago by
Michael Love
42k • written 9.2 years ago by
Nick
• 0
1
vote
2
replies
1.0k
views
DESeq Error (nbinomTest ())
Deseq
nbinomTest
4.1 years ago
canfield
▴ 10
0
votes
7
replies
2.0k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
maniermk
• 0
2
votes
5
replies
5.9k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
written 4.2 years ago by
krunal.24.6
▴ 10
2
votes
2
replies
926
views
Mocking data for understanding interactions in DESeq2
deseq2
deseq
updated 4.2 years ago by
Simon Anders
★ 3.7k • written 4.2 years ago by
blawney
• 0
3
votes
5
replies
2.2k
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 4.3 years ago by
Michael Love
42k • written 4.3 years ago by
svlachavas
▴ 830
1
vote
9
replies
1.4k
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 4.3 years ago by
Simon Anders
★ 3.7k • written 4.3 years ago by
megapode32559
• 0
0
votes
7
replies
1.3k
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2
deseq
4.4 years ago
MANYA_BIOINFO
• 0
0
votes
1
reply
1.3k
views
DESeq2 counts function not working
deseq2
Deseq
RNAseq
updated 4.6 years ago by
Michael Love
42k • written 4.6 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 4.6 years ago by
Michael Love
42k • written 4.6 years ago by
Keith Hughitt
▴ 180
4
votes
4
replies
4.7k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 4.9 years ago by
wunderl
▴ 40 • written 5.0 years ago by
neekonsu
• 0
1
vote
2
replies
958
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
sxv
• 0
0
votes
0
replies
996
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
5.0 years ago
kentfung
▴ 20
0
votes
9
replies
2.1k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
5.4 years ago
ariel
▴ 20
3
votes
12
replies
1.7k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
5.4 years ago
ariel
▴ 20
2
votes
3
replies
2.0k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
lefeverde
▴ 10
0
votes
1
reply
1.1k
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 5.7 years ago by
Michael Love
42k • written 5.7 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
5.7 years ago
Ben
▴ 50
0
votes
7
replies
4.0k
views
DESeq2 install problem
deseq
updated 5.7 years ago by
Michael Love
42k • written 5.7 years ago by
bikashten
• 0
5
votes
7
replies
3.7k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
thindmarsmission
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: limma comparison for small sample size and how to get covariance matrix
by
Gordon Smyth
51k
Your MDS plot is better than before, but you are still not following the recommendation for making for making such plots given in the limma…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data
by
Elodie
• 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
Votes
Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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