Showing : DESEQ2 • reset
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incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
3.8 years ago • updated 3.7 years ago Clay • 0
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1
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1.3k
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Controlling for sex variance in Galaxy DESeq2
DESeq2 RNASeq Galaxy
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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5
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2.5k
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from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
3.8 years ago Marianna ▴ 20
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7
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2.2k
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Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 3.8 years ago by 68k • written 3.8 years ago by ▴ 10
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1
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2.3k
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95% Confidence intervals for Fold Changes computed by DESeq2
DESeq2 RNASeq
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by • 0
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5
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1.5k
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DESeq2 - 50 vs 50 analysis
DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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3
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986
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Differentially Paired RNA-Seq Analysis DESeq2
DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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3
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1.5k
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Import RSEM output without sample data
DESeq2 tximportData tximport
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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2
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1.3k
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DEG analysis across multiple treatment condititions and different ages
DESeq2
3.8 years ago pqdugcsd • 0
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2
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2.1k
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DESeq2: Size factor estimations for type = "poscounts" different between estimateSizeFactors() and estimateSizeFactorsForMatrix()
DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 10
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1
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907
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How to solve the "tilted tail" after DESeq2 normalization.
DESeq2
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by ▴ 20
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2
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1.2k
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Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
3.8 years ago Raito92 ▴ 60
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6
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5.4k
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Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 60
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1
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1.6k
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DEGs from lfcshrink() and results()
lfcshrink DESeq2
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by ▴ 10
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1.1k
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DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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3
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1.2k
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How to get DESeq2 results in large count matix files?
DESeq2 BiocParallel MulticoreParam
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 20
3
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5
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3.6k
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Plot PC1 and PC4 in plotPCA function
DESeq2 plotPCA
updated 17 months ago by • 0 • written 3.8 years ago by • 0
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4
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1.9k
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Multi-factor paired RNAseq differential analysis with DEseq2
DESeq2 RNASeq
updated 3.8 years ago by ★ 1.4k • written 3.8 years ago by • 0
1
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1
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1.6k
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Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 20
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3
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2.0k
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ERROR: unable to find an inherited method for function ‘dispersions<-’ for signature ‘"DESeqDataSet",
DESeq2 dese
3.8 years ago aedavids ▴ 20
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3
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3.4k
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DESeq2 contrast multiple treated conditions versus multiple control conditions
RNASeq DESeq2
updated 3.8 years ago by ▴ 780 • written 3.8 years ago by • 0
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3
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2.1k
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Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 2.8 years ago by • 0 • written 3.8 years ago by • 0
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4
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2.5k
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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2
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1.4k
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Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
3.8 years ago IamFrofro • 0
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4
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1.5k
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Large DE LogFC range
DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 20
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1
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1.0k
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DESeq2 Responder vs Non-Responders nested design
paired-samples DESeq2 interactionterm nested-design
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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5
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2.4k
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Weird output of DESeq2 when using single sample from one group agains the other group (6 samples), really need some help
DifferentialExpression DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 10
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1
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1.3k
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DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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4
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1.8k
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DE analysis model matrix for paired samples
NanoStringNCTools DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 10
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3
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Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
1
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1
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1.3k
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Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 10
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1
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1.3k
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Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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2
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1.8k
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Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
3.8 years ago i.sudbery ▴ 40
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2
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2.4k
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PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 3.8 years ago by ★ 1.4k • written 3.8 years ago by • 0
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2
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2.2k
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rlog normalised count for comparing gene expression between samples
DESeq2
3.8 years ago Sam • 0
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2
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1.7k
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rlog vs vst for outlier identification
rlog DESeq2 vst outliers
3.9 years ago • updated 3.8 years ago Bex • 0
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5
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4.7k
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DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 10
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3
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1.7k
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Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 120
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1.1k
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DESeq treatment over baseline versus placebo over baseline methodology
DESeq2
3.9 years ago walter.eckalbar • 0
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3
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2.3k
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Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 3.8 years ago by 43k • written 3.9 years ago by • 0
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2
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1.1k
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DESeq2 expressed gene
DESeq2
3.9 years ago BioEpi • 0
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3
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1.3k
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Same p-adjusted value for all samples
DESeq2 p-adjusted-value Logfoldchange
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 10
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5
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2.9k
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Help with droplevels in Deseq2
droplevels DESeq2
updated 3.9 years ago by ★ 5.0k • written 3.9 years ago by ▴ 10
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8
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2.9k
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DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
3.9 years ago dadca596 • 0
3
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3
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10k
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Adding sample label to PCA plot
plotpca DESeq2
3.9 years ago bjen731 ▴ 10
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5
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1.8k
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P adjusted values in Deseq2
DESeq2 Statistics
written 4.9 years ago by • 0
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2
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4.9k
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TPM to raw counts
salmon DESeq2
updated 24 months ago by • 0 • written 3.9 years ago by • 0
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1
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1.2k
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Removal of sample data which belong to a different experiment
DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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3
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1.7k
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DESeq2: model matrix is not full rank
DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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0
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829
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Complex design in DESeq2 doesn't seem to be supported in Glimma
limma Glimma RNASeq DESeq2
3.9 years ago Jonas • 0
4,838 results • Page 24 of 97
Recent ...
Replies
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…
Answer: DESeq2 design for haplotype MPRA by aimesd808 • 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/
Answer: Extract snp information from genomic regions with biomaRt -> "oaries_snp" by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error occurs because the "chromosomal_region" filter is not valid…
Votes
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
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
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