Showing : DESEq2 • reset
1
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Too many DEGs
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 20
6
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3
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8.3k
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DESeq2 GLM modelling and Wald's test
deseq2
updated 6.5 years ago by ▴ 40 • written 6.5 years ago by ▴ 10
4
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4
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2.1k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 40
2
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2
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775
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DESeq2 positive results for genes with high samples counts dispersion
DESeq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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1
reply
1.2k
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Perform time course rna seq analysis at once with a single design or separate differential analysis for each time point
deseq2 design
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
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2
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1.2k
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Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2 vst covariates
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 20
2
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3
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26k
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Contrast for DESeq2 design with interaction and blocking factor
deseq2
6.5 years ago erwan.scaon ▴ 10
0
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3
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2.0k
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ROC curves using normalized sequencing data from 2 experiments
deseq2 pROC ROCR glm
6.5 years ago sebastian.lobentanzer ▴ 60
2
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8
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4.4k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
4
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16
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7.4k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
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1
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786
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Differential abundance analysis of 16S data with extremely unbalanced cohorts in Deseq2
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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1
reply
748
views
How can I import KEGG annotations
deseq2 annotation
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
2
votes
1
reply
665
views
Does response on subset of data in DESeq
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ★ 1.4k
0
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2
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4.2k
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Intercept result in DESeq2 two factor model
deseq2
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by • 0
0
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1
reply
563
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Package for RNA-Chromatin Interaction Matrix for Differential Gene Feature Calling?
Differential Peak Calling DiffBind DESeq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
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1
reply
622
views
DESeq2 for comparisons within group
deseq2 interaction factors complex design
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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1
reply
865
views
Using already normalized counts
deseq2
updated 6.5 years ago by ★ 13k • written 6.5 years ago by • 0
2
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6
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1.5k
views
DESeq2 analysis of no-normalized data yielded biased results
deseq2 normalization
6.5 years ago Victor Chano • 0
0
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6
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2.1k
views
how to set offset matrix to Deseq2 differential analysis
deseq2 Kallisto tximport
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
10
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20
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26k
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Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 14 months ago by 68k • written 6.5 years ago by ▴ 30
0
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3
replies
896
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Salmon / tximport
tximport deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
3
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3
replies
2.1k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
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1
reply
1.3k
views
Multiple groups and two methods to analyse them with DESeq2
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 30
0
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1
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1.4k
views
Comparing transcriptome variation across groups after Variance stabilizing transformation using DESeq2
deseq2 vst variance
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
5
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5
replies
3.1k
views
Principal components in DESeq2
deseq2
6.5 years ago Mozart ▴ 30
1
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3
replies
1.6k
views
DESeq2 gives weird results
deseq2 salmon
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
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6
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1.8k
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dseq2 results synergy contrast
deseq2 contrast synergy
updated 2.4 years ago by ▴ 10 • written 6.5 years ago by ▴ 90
0
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1
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977
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Error with DESeq2 about integer number
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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1
reply
651
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Questions about DESeq2 functionalities from beginners
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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3
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1.1k
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Shrinkage and gene ranking
deseq2
updated 3.6 years ago by 43k • written 6.5 years ago by • 0
1
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11
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1.3k
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Design formula DESeq2
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
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1
reply
2.1k
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Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
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2
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1.2k
views
DESeq2 for differential expression between species
deseq2 rna-seq
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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1
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1.0k
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
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1
reply
2.5k
views
Not integers values
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
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4
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1.2k
views
How to subset data
deseq2
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by • 0
0
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1
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588
views
DESeq2 Multi-Factor anlaysis
deseq2 multi-factor
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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3
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1.5k
views
Is Background Correction necessary before DESeq analysis
deseq2 cancer
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
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5
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1.5k
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DESEQ2 design matrix for double knockout interaction with condition
deseq2 model.matrix design matrix
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
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4
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1.4k
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DESeq2:Why is there an oblique line in my MA picture, which happened before, what caused this?
deseq2 cancer
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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8
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1.7k
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Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
4
votes
1
reply
1.5k
views
Correlation of gene expression values using tpms and normalized counts
tximport deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 20
0
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1
reply
800
views
Phylpseq to deseq2
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
2
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5
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3.1k
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DESeq2 complex model matrix and result interpretations
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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4
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1.4k
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DESeQ2 design multiple conditions
deseq2
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by • 0
2
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4
replies
2.8k
views
How to get the regression slope coefficient from DESeq2 analysis of continuous data
deseq2
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
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6
replies
2.3k
views
Plot genes with similar expression patterns
deseq2 R RNASeq
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
3
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1
reply
2.4k
views
Tximport and pseudo alignment with Kallisto
kallisto tximport deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
0
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3
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2.5k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
6.6 years ago Zach Brehm • 0
2
votes
1
reply
2.7k
views
Understanding Likelihood ratio test
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
4,840 results • Page 50 of 97
Recent ...
Replies
Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
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.
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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