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DEseq2
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News:
Course in Berlin- Genomics with R and Bioconductor - September 16-20
deseq2
edger
limma
News
6.3 years ago
info
▴ 10
1
vote
2
replies
840
views
abnormal deseq2 normalization
deseq2
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
Charls
• 0
5
votes
3
replies
1.7k
views
DESeq2 with multiple treatments but no replicates
deseq2
rna-seq
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
jpc41
▴ 20
1
vote
1
reply
2.4k
views
DESeq2 test LRT or WALD
deseq2
LRT
WALD
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
annesoalvarez
• 0
0
votes
2
replies
1.8k
views
lfcShrink in DESeq2
deseq2
apeglm
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
Meghdad
• 0
1
vote
1
reply
1.8k
views
Using RUVs with known batches
ruvseq
deseq2
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
Frederik Ziebell
▴ 30
4
votes
4
replies
6.1k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 6.3 years ago by
wunderl
▴ 40 • written 6.4 years ago by
neekonsu
• 0
2
votes
4
replies
1.0k
views
understanding DEseq2 interactions before/after releveling the baseline
deseq2
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
assaf www
▴ 140
1
vote
1
reply
1.3k
views
Request for offset slot in DESeqDataSet objects
deseq2
EDASeq
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
jeroen.gilis
▴ 100
1
vote
2
replies
973
views
appropriate design formula
deseq2
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
mr6518849
▴ 10
2
votes
4
replies
1.1k
views
Identifying cell line-independent DEG in a time series (DESeq2)
deseq2
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
jhnwphillips
• 0
0
votes
4
replies
2.8k
views
DESeq2 pairwise comparison vs contrast function
deseq2
6.3 years ago
dequattro.concetta
▴ 10
1
vote
2
replies
1.3k
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
sxv
• 0
0
votes
3
replies
1.1k
views
could the result of DEseq2 by LRT be used in SPIA directly?
deseq2
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
qq809825706
▴ 10
5
votes
13
replies
9.5k
views
DESeq2 for multiple groups
deseq2
updated 6.3 years ago by
Steve Lianoglou
★ 13k • written 6.3 years ago by
ijvechetti
▴ 10
3
votes
5
replies
1.2k
views
Multifactor design in DESeq2 - infection effect over time on three different plant cultivars
quinoa
virus
mutifactor design
DESeq2
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
n85825
• 0
0
votes
4
replies
2.0k
views
Extract residuals from DESeq2 fit
deseq2
residuals
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
MWSchmid
• 0
0
votes
2
replies
5.4k
views
Heatmap of selected genes
heatmap
DEGs
RNAseq
DESeq2
updated 6.3 years ago by
mikhael.manurung
▴ 280 • written 6.3 years ago by
danikadigiacomo
• 0
1
vote
7
replies
2.8k
views
How to merge two tximport object into one dataset for DESeqDataSetFromTximport
deseq2
tximport
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
rensanhao
• 0
8
votes
8
replies
13k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2
DESeq2
updated 2.2 years ago by
jd774
• 0 • written 6.4 years ago by
krassowski.michal
▴ 40
3
votes
3
replies
1.3k
views
DESeq2: Sample outlier patterns 'switching' after normalization
deseq2
normalization
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
wunderl
▴ 40
1
vote
4
replies
1.2k
views
Interpretation of the heatmap produced by DESeq2
DESeq2
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
yh362
• 0
1
vote
2
replies
673
views
too few replicates to observe statistically significant differences
deseq2
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
dennism9251
• 0
1
vote
3
replies
1.1k
views
deseq2 formula design
deseq2
updated 6.4 years ago by
swbarnes2
★ 1.4k • written 6.4 years ago by
Jitendra
▴ 10
1
vote
7
replies
1.9k
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2
rlog
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
mschmidt
▴ 10
0
votes
7
replies
1.0k
views
DESeq2 analysis for low RNA input
deseq2
6.4 years ago
capricygcapricyg
▴ 10
2
votes
3
replies
2.2k
views
RNAseq and heatmap
deseq2
RNA-seq
Heatmap
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
Merlin
▴ 10
1
vote
2
replies
1.3k
views
Random effects in DESeq2
deseq2
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
c.taylor
• 0
0
votes
6
replies
1.5k
views
DESeq2: Error when correcting batch effect
deseq2
batch effect
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
Rimma
• 0
2
votes
5
replies
1.9k
views
DESeq2-result files (.csv): Is there a convention for the IDs (e.g. gene names if produced for genes)
deseq2
gene
format
6.4 years ago
miriam.mueller
• 0
3
votes
7
replies
1.5k
views
Questions for ResultsNames() and the Contrast function
deseq2
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
dennism9251
• 0
8
votes
1
reply
11k
views
What can I do if I only have TPM but not raw counts data?
deseq2
updated 6.4 years ago by
Steve Lianoglou
★ 13k • written 6.4 years ago by
Di Yang
▴ 30
5
votes
5
replies
6.2k
views
tximport transcript missing
deseq2
salmon
tximport
6.4 years ago
mr6518849
▴ 10
0
votes
4
replies
904
views
DESeq2 nested effect with 5 variables
deseq2
RNA-seq
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
sandeep.amberkar18
▴ 10
4
votes
4
replies
1.3k
views
normalization of RNA-seq data after over-expressing the transcription factors
limma
deseq2
voom
edgeR
updated 6.4 years ago by
Aaron Lun
★ 29k • written 6.4 years ago by
Bogdan
▴ 670
0
votes
1
reply
813
views
Incorrect DESeq2 Output
deseq2
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
umajs
• 0
0
votes
6
replies
1.4k
views
DESeq2: Contrasts in multifactor design with interaction terms
r
deseq2
6.4 years ago
arielle
• 0
0
votes
2
replies
1.4k
views
Contrast vs relevel (DESEq2)
deseq2
RNAseq
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
Merlin
▴ 10
0
votes
3
replies
2.9k
views
DESeq2 more than 2 groups comparison
deseq2
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
sstankovic
• 0
2
votes
3
replies
1.2k
views
collapseReplicates changes the order of the original dataframe in DESeq2
deseq2
collapseReplicates
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
gtechbio
▴ 10
0
votes
7
replies
6.1k
views
DEseq2 ncol(countData) == nrow(colData) is not TRUE Error
deseq2
6.4 years ago
trumbia
• 0
0
votes
4
replies
3.6k
views
deseq2 correction batch effect without design
deseq2
batch effect
updated 6.4 years ago by
swbarnes2
★ 1.4k • written 6.4 years ago by
mdidish
• 0
1
vote
1
reply
1.3k
views
Deciphering Wilkinson Notation and Predictor Variables
deseq2
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
dennism9251
• 0
0
votes
4
replies
817
views
DESeq2 "Not full rank" Error
deseq2
updated 6.4 years ago by
swbarnes2
★ 1.4k • written 6.4 years ago by
DakJackson
• 0
1
vote
8
replies
1.8k
views
log2foldchange vs density plot from likelihood and posterior
deseq2
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
n.naharfancy
• 0
5
votes
11
replies
4.5k
views
DESeq2 logfoldchange and interaction in model
deseq2
R
logfoldchange
rna-seq
6.5 years ago • updated 6.4 years ago
pierre.marin
• 0
0
votes
1
reply
1.0k
views
RNASeq biplot variables and samples
deseq2
rnaseq
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
ecg1g15
▴ 30
0
votes
5
replies
2.6k
views
RNA-seq time course analysis with only one experimental condition
deseq2
cancer
rna-seq
time-series
6.4 years ago
mah19
• 0
1
vote
9
replies
2.6k
views
Comparing two different sequencing method by DEseq2
deseq2
updated 6.4 years ago by
swbarnes2
★ 1.4k • written 6.4 years ago by
n.naharfancy
• 0
1
vote
3
replies
2.8k
views
DESeq2: name and contrast arguments return partially different results under specific circumstances -- bug?
deseq2
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
Vincent de Bakker
• 0
4,840 results • Page
48 of 97
Recent ...
Replies
Comment: upstream git branches of bioc-release
by
TrentonCollier99
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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