Showing : DEseq2 • reset
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Appropriate DESeq2 design for multi-factor comparison within group?
deseq2 deseq
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 20
5
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4
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9.9k
views
Choosing a threshold for minimum counts in RNAseq
rnaseq deseq2
updated 8.0 years ago by 43k • written 9.5 years ago by ▴ 20
0
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1
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1.6k
views
PCA on deseq2 gene data set
pcaexplorer genespca deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
5
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19
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7.3k
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lfcShrink and factors with multiple levels
deseq2 lfcshrink relevel
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 110
3
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5
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1.8k
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DESeq2 biais when genes are missing from the annotation?
rnaseq deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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1
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1.1k
views
Deseq2 independent filtering not relevant for my data?
deseq2
updated 8.1 years ago by 43k • written 10.2 years ago by ▴ 10
4
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7
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3.5k
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GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 8.1 years ago by 43k • written 8.9 years ago by ▴ 10
2
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1
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2.7k
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deseq 2x2: highly variable genes are not among differentially expressed gene
deseq2 rld pheatmap dds
updated 8.1 years ago by 43k • written 10.2 years ago by ▴ 10
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2
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2.0k
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stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 8.1 years ago by 43k • written 10.0 years ago by ★ 1.5k
1
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3
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2.0k
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DESeq2 product of sizeFactors is not 1
deseq2 sizeFactors
updated 8.1 years ago by 43k • written 9.7 years ago by ▴ 10
2
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5
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2.0k
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DEGs generation parameters and specificities
deseq2 results design and contrast matrix
updated 8.1 years ago by 43k • written 8.6 years ago by • 0
0
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12
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2.4k
views
DESeq2 different versions
rnaseq r deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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1
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1.4k
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zero counts and deseq2
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
1
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7
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2.0k
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Strange distribution of logFC
edger deseq2 rnaseq differential gene expression
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 20
0
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1
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1.9k
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Distribution of transformed data using VST
variancestabilizingtransformation deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 80
1
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2
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2.2k
views
DGE analysis with TMM and gene length normalized data.
edger deseq2 tmm normalised values
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
1
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4
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1.2k
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Bypass dispersion estimation in DESeq2
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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3
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1.4k
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Analysis with DESeq2: should I put all the samples from three conditions in the ColData and CountData or perform the analysis separately
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 20
4
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7
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1.9k
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Altering design following DESeqDataSetFromMatrix and DESeq
deseq2 differential binding analysis
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 60
1
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2
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1.6k
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R packages old versions
R deseq2 package
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
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7
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2.7k
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DESeq2 normalization and group-wise or pair-wise comparisons
deseq2
8.1 years ago bge • 0
3
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3
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2.6k
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DESeq2 combining factors in contrasts
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 30
4
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11
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1.6k
views
2 cells X 2 conditions X patients
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
0
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1
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624
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Deseq2 for small matched samples
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 80
4
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6
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29k
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Design model for DESeq2 analysis
deseq2 differential gene expression
updated 8.1 years ago by ▴ 690 • written 8.1 years ago by ▴ 20
1
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3
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1.5k
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Matrix is not full rank with Multifactorial Experiment and Time course
deseq2 multiple factor design model.matrix time course
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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4
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2.9k
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Adaptation of DESeq/edgeR model for CRISPR drop-out screen
crispr edger deseq deseq2
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
1
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3
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1.6k
views
Structure of DiffBind dba.count matrix equivalent to DESeqDataSetFromMatrix input?
deseq2 diffbind
updated 8.1 years ago by ★ 5.2k • written 8.1 years ago by ▴ 60
3
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2
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1.1k
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DESeq2 'results' usability issue
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 690
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14
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5.4k
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Using name parameter in DESeq2-results function
deseq2 rnaseq
8.1 years ago muratcokol • 0
0
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3
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2.0k
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DESeq2 output number of genes padj <0.1 is 0?
deseq2 adjusted pvalue
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 20
0
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2
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934
views
Write table returning the same number of DEGs for different conditions. Why?
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
6
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6
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3.9k
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Comparing one condition to multiple others using DESeq2 contrasts
deseq2
updated 8.1 years ago by 21k • written 8.1 years ago by ▴ 20
16
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12
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9.3k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 15 months ago by • 0 • written 9.7 years ago by ▴ 60
0
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1
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2.0k
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DESeq2: error with DESeqDataSet function
deseq2 error DESeqDataSet DESeqDataSet
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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2
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1.4k
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Will large differences in the number of reads between samples decrease reliability of DESeq2 analysis?
deseq2
updated 8.1 years ago by ★ 7.9k • written 8.1 years ago by ▴ 10
2
votes
5
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2.4k
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calculating logfold change from variance stabilizing transformation
deseq2 logfoldchange variancestabilizingtransformation
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 80
0
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2
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1.9k
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normalizationFactors DESeq2 package
deseq2 Tutorial
updated 8.1 years ago by 53k • written 8.1 years ago by • 0
5
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7
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8.6k
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DESeq2 dispersion and p-value histograms
deseq2 rnaseq fdrtool dispersion
updated 8.1 years ago by ▴ 610 • written 8.1 years ago by ▴ 70
1
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2
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1.0k
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Pre-filtering DESeqDataSetFromMatrix input
deseq2 differential binding analysis
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 60
0
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1
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1.2k
views
'DESeqDataSetFromTximport' not found
deseq2
8.1 years ago zhizhon • 0
0
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4
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1.0k
views
Using DESeq2 for DEG.
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
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4
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2.9k
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DESEQ2 LFC calculation
deseq2
8.1 years ago amalthomas111 • 0
0
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8
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2.2k
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Time course experiments
deseq2 timecourse
8.1 years ago uu2110 • 0
1
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4
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4.2k
views
Reordering factor levels in DESeq2 causes results error in cleanContrast
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 40
2
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8
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3.7k
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comparing strand-specific counts to unstranded counts
rnaseq strand deseq2
8.1 years ago lirongrossmann ▴ 80
0
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1
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760
views
Deseq2 group comparison
rnaseq deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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2
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596
views
rlog value changed with the same input count matrix between 2015 and 2017
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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3
replies
3.0k
views
Quantile normalization and Deseq2
quantile normalization deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 80
0
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1
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2.6k
views
DESeq2: plotCounts axis labels
deseq2 graphs
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 230
4,840 results • Page 70 of 97
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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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