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DESEQ2
•
reset
12
votes
14
replies
39k
views
DESeq2 normalization vs VST vs rlog
deseq2
updated 3.0 years ago by
Jiahua
• 0 • written 6.3 years ago by
Jonas B.
▴ 40
0
votes
3
replies
2.2k
views
It takes a so long time to run DESeq2 on 1000 samples
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
Ruifeng
• 0
0
votes
1
reply
1000
views
DESeq2 design help
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
gitanjali
• 0
0
votes
4
replies
1.2k
views
Inflation of zero or low counts in one condition - is DESeq2 with ZINB-WaVE an appropriate tool for such data?
DESeq2
4.5 years ago
miyakokodama
• 0
0
votes
1
reply
1.2k
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
pthom010
• 0
2
votes
1
reply
1.5k
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq
Salmon
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
Mikołaj
• 0
1
vote
2
replies
756
views
Different P-Adjusted Values In DESeq2 for the same comparaison
RNASeq
DESeq2
4.5 years ago
fernandogs97
▴ 10
0
votes
1
reply
541
views
Dispersion Factors Not Being Calculated For Every Gene
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
rohitghosh
• 0
0
votes
1
reply
1.2k
views
DESeq2 Design matrix
StatisticalMethod
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
Saif
• 0
1
vote
2
replies
912
views
Technical reps
RNASeq
DESeq2
updated 4.5 years ago by
ATpoint
★ 5.0k • written 4.5 years ago by
Amali Thrimawithana
• 0
4
votes
7
replies
2.5k
views
Controlling for Batch Effect and Grouping in DESEQ2
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
Bine
▴ 50
0
votes
4
replies
7.4k
views
Problems installing DESeq2
DESeq2
4.5 years ago
kvitt_silver
• 0
1
vote
2
replies
1.7k
views
Grouping DESEQ2 with additional variable
DESeq2
4.5 years ago
Bine
▴ 50
2
votes
2
replies
2.3k
views
Why does limma want log2 intensities but DESeq2 use raw counts?
limma
DifferentialExpression
DESeq2
4.5 years ago
tjbencomo
• 0
0
votes
1
reply
1.4k
views
DeSeq2 with 2 conditions and 3 time points
deseq2
timepoints
updated 4.5 years ago by
swbarnes2
★ 1.4k • written 4.5 years ago by
ayy2110
• 0
2
votes
11
replies
2.0k
views
phenotypic table for DESeqDataSetFromHTSeqCount
DESeq2
4.5 years ago
rbenel
▴ 50
2
votes
2
replies
934
views
DESEQ2 colData object
DESeq2
4.5 years ago
Bine
▴ 50
7
votes
3
replies
2.1k
views
Effect of feature number on adjusted p-values
edgeR
DESeq2
single-cell
scRNAseq
zinbwave
updated 4.5 years ago by
Aaron Lun
★ 29k • written 4.5 years ago by
vincent.croset
▴ 20
2
votes
6
replies
2.0k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2
cqn
EDASeq
4.5 years ago
Saulius
▴ 10
0
votes
3
replies
1.5k
views
DESeq2 ashr with and without reflevels generate different log2FoldChanges
DESeq2
RNASeq
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
sofiagreen72211
▴ 10
0
votes
2
replies
779
views
DEseq2 nested multi factor no replicates
DESeq2
4.5 years ago
melissa.mageroy
• 0
0
votes
2
replies
2.4k
views
How to plot gene counts using plotCounts() with just an individual contrast?
DESeq2
plotCounts
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
elizabethe819
• 0
0
votes
3
replies
2.7k
views
Error installing Deseq2
DESeq2
R
4.5 years ago
GA
▴ 10
1
vote
2
replies
1.2k
views
DESeq2 desing formula for cell fraction and siRNA scramble
DEGseq
DESeq2
Designformula
updated 4.6 years ago by
swbarnes2
★ 1.4k • written 4.6 years ago by
Nicolò
• 0
4
votes
3
replies
2.5k
views
DESeq2 multiple conditions, time points and sample types
DESeq2
updated 4.5 years ago by
Wolfgang Huber
★ 13k • written 4.6 years ago by
deseq2man
• 0
1
vote
5
replies
1.2k
views
DESeq2 with high range of within-group variability
DESeq2
4.6 years ago • updated 4.4 years ago
Tash.
• 0
2
votes
2
replies
2.1k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA
DESeq2
RUVSeq
removebatcheffect()
4.6 years ago
elizabethe819
• 0
0
votes
2
replies
1.1k
views
extracting within time-point differences from time-series model
DESeq2
TimeCourse
4.6 years ago
serpalma.v
▴ 60
0
votes
4
replies
2.8k
views
Number of DEGs with adj pvalue < 0.05
DESeq2
4.6 years ago • updated 4.5 years ago
GlycineMax
• 0
1
vote
2
replies
882
views
How to average DESeq2’s median of ratios from replications
DESeq2
4.6 years ago
Yosapol
• 0
0
votes
6
replies
1.7k
views
Problem with Tximport to DESeq2
TxDb.Mmusculus.UCSC.mm10.ensGene
DESeq2
tximport
4.6 years ago
zli1
• 0
0
votes
4
replies
1.6k
views
subtracting or normalizing RNAseq reads when samples have contaminating reads
Normalization
RNASeq
contamination
edgeR
DESeq2
4.6 years ago
Yuqia
• 0
5
votes
18
replies
4.2k
views
DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow
DESeq2
GeneExpression
updated 4.5 years ago by
Michael Love
43k • written 4.6 years ago by
Yosapol
• 0
8
votes
2
replies
10k
views
handling outliers with DESeq2
RNASeqData
DESeq2
Outliers
4.6 years ago
paty
▴ 60
1
vote
6
replies
3.4k
views
The correlation between normalized counts and TPM based on 2-factor analysis by DESeq2
DESeq2
RNASeq
4.6 years ago
hequn
• 0
0
votes
8
replies
3.1k
views
DESeq2 coefficient names
resultsNames
DESeq2
coefficient
4.6 years ago
Jane
▴ 10
1
vote
5
replies
4.1k
views
Deseq2 - removing batch effect
BatchEffect
DESeq2
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
vinisha
• 0
3
votes
2
replies
1.5k
views
DESeq2 for TRAP-seq methods
DESeq2
TRAP-seq
4.6 years ago
marypiper
▴ 20
3
votes
3
replies
1.3k
views
DESeq2 unmix function
DESeq2
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
Sam
▴ 10
6
votes
3
replies
2.1k
views
Which DESeq normalization method?
DESeq2
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
save
▴ 20
0
votes
1
reply
710
views
Correcting partially penetrant batch effect
DESeq2
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
swbarnes2
★ 1.4k
1
vote
1
reply
932
views
plotMA difference using or not a sub matrix
matrixsubset
DESeq2
plotMA
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
l.troxler
▴ 10
1
vote
9
replies
7.2k
views
DESeq problems
help
DESeq2
DESeqDataSetFromMatrix
rownames
updated 3.5 years ago by
Sanatan
• 0 • written 4.6 years ago by
dorina.jamniczky
• 0
0
votes
6
replies
2.0k
views
Sample quality weights for RNA-seq
DESeq2
limma
weight
4.6 years ago
Naomi Altman
★ 6.0k
1
vote
15
replies
3.8k
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
4.6 years ago
demisa
• 0
3
votes
3
replies
1.7k
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics
DESeq2
Metatranscriptomics
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
Tom
• 0
0
votes
10
replies
2.2k
views
Problem with estimateSizeFactors due to avgTxLength
DESeq2
4.6 years ago
Mark
• 0
1
vote
1
reply
1.9k
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks
RECOUNT2
DESeq2
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
xiaofeiwang18266
▴ 60
4
votes
4
replies
4.2k
views
DESeq2 two conditions with interaction
DESeq2
updated 4.6 years ago by
swbarnes2
★ 1.4k • written 4.6 years ago by
mboeck
• 0
0
votes
1
reply
1.2k
views
DEseq2 to test half-life for time-series data
half-life
DESeq2
time-series
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
Xianjun Dong
▴ 10
4,839 results • Page
30 of 97
Recent ...
Replies
Comment: Post translational modifications and phosphoproteomics in limpa?
by
james.eapen
• 0
Thank you!
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
ATpoint
★ 5.0k
The donor effect is crystal clear, and absent in these suspicious samples. It strongly argues for a technical problem. If you really need s…
Answer: mzR-Rcpp compiler version issue
by
Laurent Gatto
1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co
by
jamie.gearing
▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria
by
Stefano Mangiola
▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Votes
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
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