Showing : DESEQ2 • reset
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DESeq2 experimental design
deseq2 multiple factor design
updated 8.1 years ago by ▴ 690 • written 8.1 years ago by ▴ 10
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3
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1.7k
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DESeq: large difference in number of replicates per condition
deseq2 rnaseq differential expression
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
4
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2
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2.7k
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Within-sample gene comparison with DESeq2
deseq2 normalization
8.1 years ago ctruntzer ▴ 20
6
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3
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4.9k
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DESeq2 contrast using list
deseq2
updated 8.1 years ago by ▴ 690 • written 8.1 years ago by ▴ 20
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4
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1.4k
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Missing design when using Scran to create a DESeqDataSet
deseq2 Scran
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
3
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5
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DESeqDataSetFromTximport with kallisto abundances.
deseq2 tximport
updated 8.1 years ago by • 0 • written 8.5 years ago by ▴ 30
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2
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1.4k
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QIIME Differential abundance on multiple studies
deseq2 qiime
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
5
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4
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1.9k
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Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 10
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4
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2.8k
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How to get an output from DESeq2 to be used in WGCNA package
deseq2 wgcna
updated 8.1 years ago by ★ 3.0k • written 8.1 years ago by • 0
2
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1
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1.1k
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combine two differential expression methods
edger deseq2 dea publish
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
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7
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2.9k
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Deseq2 no package Matrix found
deseq2 bioconductor matrix
8.2 years ago victoria.carla.moris • 0
5
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12
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7.0k
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DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 4.1 years ago by ▴ 30 • written 8.2 years ago by ▴ 40
6
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3
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4.8k
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Add new columns to DESeqResults from text file by matching rownames.
deseq2 deseq merge data frames cbind s4vectors
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
26
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7
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Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 20
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4
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RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
rangedsummarizedexperiment deseqdatasetfrommatrix deseq2 tximport
8.2 years ago lirongrossmann ▴ 80
2
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4
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1.6k
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Error in tximport, unused argument (reader = read_tsv)
tximport deseq2
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
0
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6
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4.2k
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Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
8.2 years ago lirongrossmann ▴ 80
1
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4
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24k
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Adjusting for covariates in paired sample design DESeq2
deseq2 deseq paired samples covariates multiple time points
8.2 years ago imb ▴ 10
6
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19
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5.2k
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Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by ▴ 50
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14
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Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 90
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3
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deseq2 vst transformation
deseq2 variancestabilizingtransformation
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
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3
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767
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DESeq2 Which gene used to normalize?
deseq2 normalization R
updated 8.2 years ago by ★ 13k • written 8.2 years ago by • 0
8
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12
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5.0k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 8.2 years ago by ★ 2.1k • written 8.2 years ago by • 0
2
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12
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6.4k
views
DESeq2 Dispersion Shrinkage - more samples is better?
deseq2 DDS
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 70
3
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2
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1.3k
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DESeq2 Design Formula for Time Series Experiment
deseq2
updated 8.2 years ago by ▴ 20 • written 8.2 years ago by ▴ 10
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4
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5.9k
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About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
8.2 years ago David Requena ▴ 20
10
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6
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5.5k
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Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq deseq2 edger voom limma
updated 8.2 years ago by ▴ 110 • written 10.5 years ago by 21k
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4
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8.0k
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Sample-to-sample distance matrix using heatmap.2
heatmap.2 gplots DESeq2
8.2 years ago Jane Merlevede ▴ 90
2
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3
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1.4k
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problem with DESeq2 on metagenome analysis
deseq2 metagenome
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
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1
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2.0k
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DESeq2 biological replicates and RIN values
deseq2 differential gene expression covariates rnaseq
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
2
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1
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1.3k
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[DESeq2] Slight difference between lfcMLE and my calculated log2 fold change
deseq2
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
0
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5
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1.1k
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paired design with continious covariate
deseq2 r
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
1
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3
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1.5k
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DESeq2 for ASE
DESEQ2 ASE diploid-genome
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
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4
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1.1k
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Effect of inclusion of patientID in the formula
deseq2
updated 8.2 years ago by 68k • written 8.2 years ago by ▴ 10
0
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1
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1.8k
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Importing kallisto's abundance files into DESeq2 pipeline
deseq2 kallisto
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
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19
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2.8k
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Paired Difference Analysis
deseq2 R differential gene expression
8.3 years ago • updated 8.2 years ago nhua • 0
1
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1
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7.7k
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DESeq2 had non-zero exit status
deseq2
updated 8.2 years ago by ★ 6.6k • written 8.2 years ago by ▴ 10
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3
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2.0k
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DESeq2 ComputeSumFactors extract normalized counts
deseq2 normalization counts
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
1
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8
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3.8k
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How to exactly replicate the results from plotMA in DESeq2 ?
deseq2 plotma
8.2 years ago Yvan Wenger ▴ 50
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9
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2.6k
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lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2 lfcshrink rlog
8.2 years ago pecot • 0
2
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1
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1.8k
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DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2 lrt
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by • 0
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11
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2.2k
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Looking at interaction term in DESeq2 while also controlling for individual variable
deseq2
8.2 years ago hmgeiger ▴ 10
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2
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3.7k
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DESeq2 Design controlling for gender
deseq2 multiple factor design
written 8.2 years ago by • 0
5
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2
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4.7k
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deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 lrt wald differential gene expression
updated 3.7 years ago by • 0 • written 8.2 years ago by • 0
0
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1
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1.3k
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DESeq2 with 4 groups, 5 timepoints and more...!
deseq2 biomarkers
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by • 0
2
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3
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1.1k
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interaction between continious and categorical variables
deseq2 r
8.2 years ago fabian.roger • 0
2
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13
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3.8k
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DESeq2 and betaPrior
deseq2 biostatistics
8.2 years ago Elena Grassi ▴ 10
5
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2
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4.2k
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Interaction term - Model matrix not full rank
deseq2 interaction term
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
3
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2
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4.3k
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DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
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1
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1.3k
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how to select a result output from multiple factor design in deseq2
deseq2
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
4,839 results • Page 72 of 97
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Comment: limpa - drivers for unusually high standard error? by Julia Broadbent • 0
Apologies for not being clearer in my initial question, but thank you for answering regardless! The large SE values I am looking at appear …
Answer: limpa - drivers for unusually high standard error? by Gordon Smyth 53k
Hi Julia, I am going to assume that you mean standard errors (SEs) returned by `dpcQuant()`, because later stages in the limpa pipeline do…
Comment: gene Set with high AUC score but no cells assigned to cell type by e.j.aaw.g.erm • 0
It sounds like AUCell is struggling with thresholding because your cDC2 gene set doesn t show a clear bimodal distribution. While a high AU…
Comment: featureCounts -L: high unassigned:mapq fraction by insurancetaaddddaxrealty • 0
FeatureCounts can behave differently with ONT cDNA BAM files due to long read splice patterns, and many users compare settings or presets m…
Comment: A problem occurs when running the monocle2 by e.j.aaw.g.erm • 0
For gamers facing technical issues or errors in complex scripts, the Redz Hub script download provides a reliable tool to optimize performa…
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Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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
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