Showing : deseq2 • reset
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Batch effects removal across mRNA seq studies addressing different biological question: Best approach?
DESeq2
21 months ago Kuldeep • 0
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by • 0
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DESeq2 lfcShrink drastic shrinkage
DESeq2
updated 6 months ago by • 0 • written 21 months ago by • 0
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
21 months ago island • 0
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DESeq2 aborting after upgrade
DESeq2
21 months ago • updated 20 months ago Aarti • 0
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Cross-species analysis using DESeq2 - size factor computation
dese DESeq2
21 months ago pl23 • 0
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 21 months ago by • 0
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Regressing out covariates from expression matrix for PCA visualization - can I use coefficients calculated in DESeq2??
DESeq2
21 months ago tombate94 • 0
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1.1k
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
21 months ago Jawahar • 0
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805
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Which fasta files to use for tximeta makeLinkTxome
tximeta DESeq2
21 months ago JING • 0
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523
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DESEQ2 reduced model input into Pathfindr
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
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726
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 21 months ago by 43k • written 21 months ago by • 0
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Deleting a column from data frame and then running DESeq2
DESeq2
updated 21 months ago by 43k • written 21 months ago by ▴ 10
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Plotting mean TPM of an expressed gene
DESeq2
21 months ago mp52226 • 0
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Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
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589
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[DESEQ2] When to average biological replicates for hierarchical clustering
DESeq2
updated 21 months ago by 68k • written 21 months ago by • 0
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604
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How to interpret log2fold values when using numeric contrasts in DESEQ2?
DESeq2
21 months ago pl23 • 0
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652
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Looking for a MSigDB chip file
DESeq2
updated 21 months ago by 68k • written 21 months ago by • 0
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DESeq2 multi-factor design and interaction terms
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
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RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
21 months ago Luca • 0
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
21 months ago WS • 0
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DESeq2 design with multiple factors
DESeq2
written 21 months ago by • 0
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 21 months ago by 43k • written 22 months ago by • 0
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1.2k
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 22 months ago by • 0
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
22 months ago • updated 21 months ago Linton • 0
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5
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1.9k
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 21 months ago by ★ 5.0k • written 22 months ago by • 0
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973
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DESeq2 interaction term + sva
sva DESeq2
updated 22 months ago by 43k • written 22 months ago by ▴ 20
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
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938
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
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Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 22 months ago by ★ 1.4k • written 22 months ago by • 0
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1.4k
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Deseq2 Coefficients from resultsNames() not reflecting all coefficient possibilities.
DESeq2
22 months ago • updated 20 months ago JalapenoCornbread • 0
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lfcSE always positive. Does this make sense?
DESeq2
updated 22 months ago by 21k • written 22 months ago by • 0
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849
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DESeq2: Difference in DEG numbers when switching reference condition (numerator, denominator) using contrast
DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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1.7k
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DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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1.1k
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DESeq2: the model matrix is not full rank issue
DESeq2
updated 22 months ago by • 0 • written 22 months ago by • 0
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2.2k
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Difference between vst() and varianceStabilizingTransform()
DESeq2
written 22 months ago by • 0
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5
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1.2k
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Unexpected results for a differential expression analysis between males and females
DESeq2
updated 22 months ago by ★ 3.4k • written 22 months ago by • 0
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5
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2.3k
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scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?
pseudobulk seurat DESeq2
updated 22 months ago by ★ 4.0k • written 22 months ago by • 0
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1.2k
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 21 months ago by 53k • written 22 months ago by • 0
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778
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Running DESeq on normalized data
deseq DESeq2
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
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1.1k
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Linear Model Fitting and Colinearity
dese DESeq2
22 months ago Hugo • 0
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1
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615
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removeBatchEffect with non-linear model fit
limma DESeq2
updated 22 months ago by 53k • written 22 months ago by • 0
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13
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2.4k
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Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions replicates SmallRNAData DESeq2
updated 21 months ago by ★ 4.0k • written 22 months ago by ▴ 10
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1
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1.6k
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 22 months ago by 68k • written 22 months ago by • 0
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847
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 8 weeks ago by ▴ 10 • written 23 months ago by • 0
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DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink GSEABenchmarkeR DESeq2
updated 22 months ago by ★ 5.0k • written 23 months ago by • 0
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1.8k
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How does Deseq2 deal with the row with zero when calculating size factors
DESeq2
written 23 months ago by • 0
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tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 23 months ago by 68k • written 23 months ago by • 0
4,835 results • Page 8 of 97
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Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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