Showing : DEseq2 • reset
12
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14
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40k
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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
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3
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2.2k
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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
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1.0k
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DESeq2 design help
DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
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4
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1.2k
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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
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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
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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
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2
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762
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Different P-Adjusted Values In DESeq2 for the same comparaison
RNASeq DESeq2
4.5 years ago fernandogs97 ▴ 10
0
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1
reply
542
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
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1
reply
1.2k
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DESeq2 Design matrix
StatisticalMethod DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
1
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2
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915
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Technical reps
RNASeq DESeq2
updated 4.5 years ago by ★ 5.0k • written 4.5 years ago by • 0
4
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7
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2.6k
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
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4
replies
7.4k
views
Problems installing DESeq2
DESeq2
4.5 years ago kvitt_silver • 0
1
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2
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1.7k
views
Grouping DESEQ2 with additional variable
DESeq2
4.5 years ago Bine ▴ 50
2
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2
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2.3k
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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
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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
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11
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2.0k
views
phenotypic table for DESeqDataSetFromHTSeqCount
DESeq2
4.5 years ago rbenel ▴ 50
2
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2
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937
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DESEQ2 colData object
DESeq2
4.5 years ago Bine ▴ 50
7
votes
3
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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 4.6 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
4.6 years ago Saulius ▴ 10
0
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3
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1.5k
views
DESeq2 ashr with and without reflevels generate different log2FoldChanges
DESeq2 RNASeq
updated 4.5 years ago by 43k • written 4.6 years ago by ▴ 10
0
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2
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785
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DEseq2 nested multi factor no replicates
DESeq2
4.6 years ago melissa.mageroy • 0
0
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2
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2.4k
views
How to plot gene counts using plotCounts() with just an individual contrast?
DESeq2 plotCounts
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
0
votes
3
replies
2.8k
views
Error installing Deseq2
DESeq2 R
4.6 years ago • updated 4.5 years ago GA ▴ 10
1
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2
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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
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3
replies
2.5k
views
DESeq2 multiple conditions, time points and sample types
DESeq2
updated 4.6 years ago by ★ 13k • written 4.6 years ago by • 0
1
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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
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2
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1.1k
views
extracting within time-point differences from time-series model
DESeq2 TimeCourse
4.6 years ago serpalma.v ▴ 60
0
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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
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2
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888
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How to average DESeq2’s median of ratios from replications
DESeq2
4.6 years ago Yosapol • 0
0
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6
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1.8k
views
Problem with Tximport to DESeq2
TxDb.Mmusculus.UCSC.mm10.ensGene DESeq2 tximport
4.6 years ago zli1 • 0
0
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4
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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
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18
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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
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2
replies
10k
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handling outliers with DESeq2
RNASeqData DESeq2 Outliers
4.6 years ago paty ▴ 60
1
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6
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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
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8
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3.1k
views
DESeq2 coefficient names
resultsNames DESeq2 coefficient
4.6 years ago Jane ▴ 10
1
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5
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4.1k
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Deseq2 - removing batch effect
BatchEffect DESeq2
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
3
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2
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1.5k
views
DESeq2 for TRAP-seq methods
DESeq2 TRAP-seq
4.6 years ago marypiper ▴ 20
3
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3
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1.3k
views
DESeq2 unmix function
DESeq2
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 10
6
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3
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2.1k
views
Which DESeq normalization method?
DESeq2
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 20
0
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1
reply
712
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
936
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
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15
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3.8k
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between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
4.6 years ago demisa • 0
3
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3
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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
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10
replies
2.2k
views
Problem with estimateSizeFactors due to avgTxLength
DESeq2
4.6 years ago Mark • 0
1
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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
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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
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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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