Showing : DESEq2 • reset
1
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Differential expression between groups with zero counts in DESEQ2
zero counts deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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6
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3.0k
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DESeq2 load failed for Bioconductor ver 3.9
deseq2
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
0
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1
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1.6k
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Using DESeq2with Oxford Nanopore Technology Direct RNA Sequencing
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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1
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1.8k
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DESeq2 interaction term interpretation
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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5
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1.3k
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DESeq not showing all coefficient
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
0
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3
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2.6k
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Change order of conditions when plotting: plotCounts {DESeq2}
R deseq2 plotcounts
6.6 years ago ecg1g15 ▴ 30
2
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5
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1.4k
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Deseq2 Multivariate Time Series: DEGs for each time point comparison?
deseq2 RNA-seq
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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1
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575
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Is it possible to do joint hypothesis testing in DESeq2?
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
3
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3
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1.1k
views
What is the best deseq2 design for this situtation?
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 20
2
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4
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918
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Inclusion/exclusion of levels of a factor
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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1
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588
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Some genes are filtered after DESeq2 normalization
deseq2 normalization
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
11
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10
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5.7k
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Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a transcriptome?
deseq2 nanopore
6.6 years ago David Eccles (gringer) ▴ 30
1
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1
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3.2k
views
Advice on correcting for batch effect using DESeq2
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 140
1
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4
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1.8k
views
Complex Design matrix for DE analysis
deseq2 edger limma
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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1
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3.0k
views
Up and down regulated genes in deseq2
deseq2 up-regulated down-regulate
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
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1
reply
797
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Time Comparisons in Deseq2
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
0
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2
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2.8k
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no gene names in deseq2 result file
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
0
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3
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1.2k
views
Comparison of samples of different time points using DESeq2.
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
2
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5
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1.8k
views
DESeq2 setting significant p-value
DESeq2
updated 19 months ago by 43k • written 6.6 years ago by ▴ 10
0
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1
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1.1k
views
Robust FPM with normalization factors (from tximport)?
deseq2 tximport normalization
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
2
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3
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1.5k
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null model and DEXSeqDataSet object in DEXSEQ
deseq2 dexseq
6.6 years ago gv ▴ 40
1
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3
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30k
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z-score with DESeq2?
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 20
2
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6
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1.8k
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2 dexseq
6.6 years ago gv ▴ 40
0
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1
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678
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Question about outlier detection for continuous phenotype using DESeq2
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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1
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1.1k
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
3
votes
5
replies
2.3k
views
Using vegan::betadisper for determing if I subset my design for DESeq2
deseq2
updated 4.8 years ago by ▴ 270 • written 6.6 years ago by ▴ 20
3
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3
replies
1.5k
views
lfc shrinkage two factor experiment
deseq2 lfcShrink
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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6
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3.3k
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Problem with construction of DESeqDataSet object
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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2
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997
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Deseq2 design for repeated measure
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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1
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499
views
DESeq2 paired comparison, unexpected results
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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6
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1.4k
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DESeq2- design matrix with multiple factors, taking gender into consideration
deseq2 multifactor interaction term gender effect 3-factors
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 50
0
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1
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1.2k
views
DESeq2 Design for 2 Conditions
deseq2 r R RNA-Seq
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
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2
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1.3k
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tximport and txOut
tximport deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
0
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1
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1.7k
views
DESeqDataSetFromMatrix NA error while there is no NA in the data
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
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7
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3.4k
views
Extracting sex specific differences between groups using DESeq2 interactions?
deseq2
updated 3.7 years ago by 43k • written 6.6 years ago by ▴ 20
1
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5
replies
2.1k
views
DESeq2: differential expression analysis from matrix count with gene annotation
deseq2 dataframe pasilla
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
0
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2
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1.3k
views
DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
0
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2
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897
views
Manually feed DESeq with dispersions
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
4
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13
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2.0k
views
DESeq2: How does the model of the trend function looks like?
DESeq2 gamma-family Dispersion trend
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
2
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3
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2.2k
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Three-factor design with DESeq2
deseq2 Time-course
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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3
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1.4k
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Installing DESeq2 on Google Cloud
deseq2
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
0
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1
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669
views
DESEQ2 normalization vs Subsampling
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
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3
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2.2k
views
RPM data analysis with DESeq2
deseq2 RPM gene expression
6.6 years ago ruhollah.mb • 0
1
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3
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817
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Analyzing nested experimental conditions in DESeq2
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
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11
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8.9k
views
Unable to install packages
software error deseq2
updated 6.6 years ago by • 0 • written 6.6 years ago by ▴ 10
0
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3
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2.3k
views
Comparison of Comparisons with DESeq2
deseq2 comparison of comparisons compare two contrasts complex contrast
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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9
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1.5k
views
RNAseq analysis DeSeq2 strange MAplot
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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2
replies
892
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DESeq2_variance stabilisation (rlog/vst) on cross species samples
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
2
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1
reply
1.1k
views
DESeq2 statistic and design
deseq2 RNA
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
3
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1
reply
727
views
DESeq2 LFCshring=2 or 4
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
4,840 results • Page 51 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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