Showing : DESEq2 • reset
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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
3
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4
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2.7k
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Removing rows (countData) from a DESeq Object
DESeq2
4.7 years ago Bine ▴ 50
3
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1
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652
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Using group instead of interaction term on a custom edited matrix
DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
3
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5
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2.5k
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Deseq2 Paired Samples Design
DESeq2
4.8 years ago • updated 4.7 years ago Rita • 0
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1
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1.4k
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PCA rand heatmap of raw data
DESeq2 DiffSeq PrincipalComponent rlog heatmaps
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 30
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3
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1.4k
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Single sided P-value for DESeq2 Likelihood Ratio Test
DESeq2 DESe
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
6
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11
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6.5k
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How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 20 months ago by • 0 • written 4.8 years ago by ▴ 40
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2
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1.2k
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Pair-wise DESeq2 using tximport (running time and multi-threading)
tximport DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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2
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3.8k
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error in DESeq2 results(dds)
DESeq2 datasetfrommatrix results error
4.8 years ago james • 0
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4
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2.2k
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goseq package loading issues
DESeq2 goseq
4.8 years ago avinashi • 0
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2
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3.2k
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Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
4.8 years ago Nikolay Ivanov • 0
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1.1k
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error during installation of 'DEseq2' package
DESeq2 Install
updated 4.7 years ago by 16k • written 4.8 years ago by • 0
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3
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2.1k
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DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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15
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Exporting DESeq2 filtered results
DESeq2
updated 2.2 years ago by 68k • written 4.8 years ago by ▴ 10
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3
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1.2k
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deseq2 design with two variables
DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
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4
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Identifying differentially expressed genes
identifyingDifferentiallyexpressedgenes DESeq2
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by • 0
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3
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3.7k
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why does stat column disappears after lfcshrink on deseq 2 and why does fgsea uses stat column (not affected by shrinking) for fgsea?
fgsea DESeq2
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by ▴ 30
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2
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1.9k
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Gene Selection GTex for DESeq2 Analysis
DESeq2 GTEx
4.8 years ago Bine ▴ 50
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6
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1.2k
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I can't get the 2 by 2 comparisons that I need because the matrix is not full of rank
DESeq2
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by • 0
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3
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1.7k
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How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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7
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3.3k
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Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 4.5 years ago by 43k • written 4.8 years ago by ▴ 30
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3
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4.0k
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How to setup a two factor design in DESeq2
DESeq2 two-factorialdesign
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
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2
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6.4k
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Importing data into the DESeq2 pipeline using tximport
DESeq2 tximport
4.8 years ago Nikolay Ivanov • 0
4
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3
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1.6k
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Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
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3
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928
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Isolate two different condtitions from DeSeq2 object
SubsetConditions DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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3
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1.7k
views
Unable to reproduce Pasilla dataset which fresh instalation
tutorial DESeq2 pasilla
4.8 years ago Carina • 0
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1
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937
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Linear Regression Diagnostic Plots with DESeq2
DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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2
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4.6k
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Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘plotPCA’ for signature ‘"prcomp"’
plotGrouper DESeq2 plot
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by • 0
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1.7k
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Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
1
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1
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854
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Analysis design for DESeq2
DifferentialExpression DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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1.5k
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How to get the dispersion values before fitting?
DESeq2
4.8 years ago raya.fai ▴ 60
3
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4
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3.7k
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R Error: package ‘GenomeInfoDb’ could not be loaded on MacBook
error mac DESeq2 GenomeInfoDb R
4.9 years ago • updated 4.8 years ago Dan ▴ 20
6
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5
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1.7k
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perform DESeq2 based on paired sample
DESeq2
4.8 years ago xiaofeiwang18266 ▴ 60
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4
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1.6k
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DEseq2: working with unbalanced number of sample in tumor study?
Deseq2 RNASeqRData unbalancedsamplesize
updated 3.5 years ago by 43k • written 4.8 years ago by • 0
2
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2
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1.6k
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DESeq2 in R
DESeq2 apeglm
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by ▴ 10
4
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9
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2.1k
views
Variance stabilising transformation to within given range
DESeq2 scaling vst
updated 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 60
1
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2
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649
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DESeq2
DESeq2
4.8 years ago amoaristotle ▴ 10
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4
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1.4k
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DESeq2 Design formula matrix not full rank
DESeq2 matrixnotfullrank Designformula DEseq2
4.8 years ago Nicolò • 0
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2
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1.7k
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DSEQ apeglm
DESeq2 apeglm
4.8 years ago amoaristotle ▴ 10
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5
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2.6k
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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4
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2.4k
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DEseq2: setting up the correct contrast.
DESeq2 RNASeq
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by • 0
2
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1
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1.8k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 4.8 years ago by 43k • written 4.8 years ago by ★ 5.0k
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5
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2.8k
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How can I use bioconductor and Deseq2 in linux ubuntu 18
RiboProfiling DESeq2 Bioconductor RNASeqRData
updated 3.1 years ago by ★ 4.0k • written 4.8 years ago by • 0
3
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3
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2.6k
views
Normalisation in DESeq2
DESeq2
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by ▴ 50
1
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1
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1.4k
views
No result from plotPCA()
DESeq2 RNASeq plotpca
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
2
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4
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2.5k
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DESeq2 results change dramatically after scaling + centering of numeric variable
DESeq2
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 20
2
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6
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1.5k
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DESeq2 anormally high estimation of Log2FoldChange
DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
2
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3
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1.6k
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Independent filtering of NGS data
independentfiltering DESeq2 CRISPR
4.8 years ago Rubén • 0
2
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3
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2.7k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 30
3
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3
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1.6k
views
DESeq2 for time-course with nested individuals
DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
4,840 results • Page 32 of 97
Recent ...
Replies
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
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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