Showing : DESEQ2 • reset
12
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14
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39k
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DESeq2 normalization vs VST vs rlog
deseq2
updated 3.0 years ago by • 0 • written 6.3 years ago by ▴ 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 43k • written 4.5 years ago by • 0
0
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1
reply
1000
views
DESeq2 design help
DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 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
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1.2k
views
Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 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 43k • written 4.5 years ago by • 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 43k • written 4.5 years ago by • 0
0
votes
1
reply
1.2k
views
DESeq2 Design matrix
StatisticalMethod DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
1
vote
2
replies
912
views
Technical reps
RNASeq DESeq2
updated 4.5 years ago by ★ 5.0k • written 4.5 years ago by • 0
4
votes
7
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2.5k
views
Controlling for Batch Effect and Grouping in DESEQ2
DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 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 ★ 1.4k • written 4.5 years ago by • 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 ★ 29k • written 4.5 years ago by ▴ 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 43k • written 4.5 years ago by ▴ 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 43k • written 4.5 years ago by • 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 ★ 1.4k • written 4.6 years ago by • 0
4
votes
3
replies
2.5k
views
DESeq2 multiple conditions, time points and sample types
DESeq2
updated 4.5 years ago by ★ 13k • written 4.6 years ago by • 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 43k • written 4.6 years ago by • 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 ★ 4.0k • written 4.6 years ago by • 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 43k • written 4.6 years ago by ▴ 10
6
votes
3
replies
2.1k
views
Which DESeq normalization method?
DESeq2
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 20
0
votes
1
reply
710
views
Correcting partially penetrant batch effect
DESeq2
updated 4.6 years ago by 43k • written 4.6 years ago by ★ 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 43k • written 4.6 years ago by ▴ 10
1
vote
9
replies
7.2k
views
DESeq problems
help DESeq2 DESeqDataSetFromMatrix rownames
updated 3.5 years ago by • 0 • written 4.6 years ago by • 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 43k • written 4.6 years ago by • 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 43k • written 4.6 years ago by ▴ 60
4
votes
4
replies
4.2k
views
DESeq2 two conditions with interaction
DESeq2
updated 4.6 years ago by ★ 1.4k • written 4.6 years ago by • 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 43k • written 4.6 years ago by ▴ 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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