Showing : DEseq2 • reset
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Outliers
outliers Deseq2
4.6 years ago nolwenn • 0
0
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11
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2.9k
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How to setup sample design in DESeq2
DESeq2
written 4.8 years ago by ▴ 10
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12
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3.1k
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Data normalization
DESeq2 Normalization
4.6 years ago nolwenn • 0
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1
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1.1k
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Deseq2 error "Error in designAndArgChecker"
DESeq2
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 10
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2
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718
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Different genes using same method
DESeq2
4.6 years ago menuka • 0
1
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3
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1.2k
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Preferential sequencing of longer Genes in Illumina?
DESeq2 sequencing
updated 4.7 years ago by • 0 • written 4.7 years ago by • 0
2
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2
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1.2k
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is the P value reliable if the counts are Low across the sample ?
DESeq2 sequencing
4.7 years ago simplyphage • 0
2
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4
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3.5k
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How to reassign DESeqDataSet design to include newly added column to columnData
DESeq2
updated 4.1 years ago by 43k • written 4.7 years ago by • 0
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1
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1.0k
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DEseq2 for analysis of time points
DESeq2 timepoints
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 30
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3
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4.6k
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DESEQ2: Some genes have empty pvalue and padj
DESeq2
updated 4.7 years ago by ★ 5.0k • written 4.7 years ago by ▴ 50
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2
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2.4k
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Comparison when Control is in differen batch
DESeq2 DifferentialExpression
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 30
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2
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1.5k
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Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2 Nullcook'svalues 2x3 DEGs
4.7 years ago andreia ▴ 10
1
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2
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2.0k
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Biological Replicate factor in Design Formula (DESeq2)
DESeq2
4.7 years ago DcL-A • 0
0
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1
reply
992
views
Wald or LR Test
DESeq2 DifferentialExpression
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
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3
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1.5k
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DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
4.7 years ago sieminsk • 0
4
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18
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9.1k
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DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 10
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4
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1.5k
views
How sensitive is DiffBind to Deseq2 assumptions ?
DESeq2 DiffBind
updated 4.6 years ago by ★ 5.2k • written 4.7 years ago by ▴ 10
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1
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1.0k
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DESEQ2 normalization for time series data
DESeq2 Normalization Medianofratios
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
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2
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1.3k
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Using a numeric contrast vector to find genes differentially expressed by non-additive effect of a condition
DESeq2
written 4.7 years ago by • 0
2
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4
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1.4k
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DESEQ2 Formula with 5 variables
DESeq2
4.7 years ago Bine ▴ 50
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3
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1.4k
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DESEQ object filter
DESeq2
written 4.7 years ago by ▴ 50
1
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1
reply
3.2k
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DESeq2 Installation fails with non-zero exit status
DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
2
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2
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1.4k
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TxImport when quant.sf files have different index files
tximport DESeq2
4.7 years ago mprnl • 0
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4
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15k
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Problem install: Package ‘DESeq2’ is not available for this version of R
DESeq2
updated 4.7 years ago by ★ 5.0k • written 4.7 years ago by • 0
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4
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1.2k
views
replaceOutliers in DESeq2 : need to recompute size Factors ?
DESeq2
4.7 years ago eleonoregravier ▴ 70
3
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2
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1.1k
views
DeSeq2 design for sgRNA fold-change
DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 10
2
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3
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5.3k
views
Failing to install DESeq because the version is not compatible
DESeq2
updated 4.7 years ago by 4.2k • written 4.7 years ago by • 0
0
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1
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1.1k
views
Non-significant but high LFC after apeglm shrinkage
DESeq2 apeglm
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
2
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5
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5.1k
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DEGpatterns and functional analysis of clusters
DESeq2 RNASeq DEGreport
updated 3.1 years ago by 43k • written 4.7 years ago by ▴ 10
3
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5
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2.4k
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Cook's distance outlier detection
DESeq2 cook'sdistance
4.7 years ago hpapoli • 0
3
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1
reply
2.6k
views
DESeq2 fold change filtering
DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 10
1
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4
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1.1k
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DESeq2 - How can we correct for a "Group-specific condition effect" if the condition can be applied to one group only?
DESeq2
4.7 years ago Tamer ▴ 10
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4
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3.3k
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Using DESeq2 with GlmGamPoi
DESeq2 glmGamPoi scRNAseq
4.7 years ago tatyana.perlova • 0
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1
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1.2k
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Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
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2
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2.1k
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Finding the correct version of DESeq2 for my version of R (3.6.1)
error DESeq2 Install
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
7
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4
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17k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 3.9 years ago by • 0 • written 4.7 years ago by ▴ 20
0
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1
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989
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How to analyze ribosome profiling data in the form of a 2x2x2 experiment using DESeq2
DESeq2 RiboSeq RNASeq
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
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3
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1.2k
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Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
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7
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2.5k
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DESeq2: Too many "NA" for adjPvalue
DESeq2
4.7 years ago • updated 3.7 years ago sagharib • 0
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1
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1.1k
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is docker image using DESeq portable?
bioconductor/bioconductor_docker DESeq2
updated 4.7 years ago by ▴ 140 • written 4.7 years ago by ▴ 20
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6
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40k
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DESeq2 / PCA Analysis of RNA-seq Data - Best Explanatory Resource?
DESeq2 pcaExplorer
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 30
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2
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1.3k
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Negative svalues from DESeq2 lfcShrink with ashr
ashr DESeq2 lfcShrink svalue
4.7 years ago Enrico • 0
0
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1
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901
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DESeq2 calling DEGs despite detection in few replicates
DESeq2
updated 4.7 years ago by ★ 1.4k • written 4.7 years ago by • 0
0
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2
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1.3k
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DESeq2 design formula and batch correction
DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
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3
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3.9k
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
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2.2k
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An attempt to better understand DESeq2 dispersion estimation
DESeq2
4.7 years ago Sam ▴ 10
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1
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3.5k
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Biological replicates in DESeq2
DESeq2 Bioconductor RNASeqR
updated 4.7 years ago by ★ 5.0k • written 4.7 years ago by • 0
1
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3
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2.1k
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Batch correction and DESeq2
DESeq2
4.7 years ago Alessia • 0
2
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1
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731
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Splitting multiple groups - three different ages
DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
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1
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3.4k
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DESeq2, tximport normalization, normalization factors, size factors
tximport DESeq2 normalizationfactors sizefactors
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
4,839 results • Page 31 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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