Showing : DESeq2 • reset
13
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22
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26k
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DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 8 weeks ago by 41k • written 7.8 years ago by ▴ 30
28
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21
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48k
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deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.2 years ago by ▴ 40
5
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18
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7.4k
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Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 4 months ago by • 0 • written 2.2 years ago by • 0
2
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17
replies
1.7k
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lfcshrink error DESeq2
DESeq2 lfcshrink DESe
updated 11 months ago by 41k • written 11 months ago by • 0
0
votes
17
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3.4k
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What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 10 months ago by • 0 • written 6.6 years ago by • 0
3
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16
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2.1k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 3 months ago by 3.8k • written 2.8 years ago by ▴ 10
6
votes
16
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2.2k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by 41k • written 4.6 years ago by ▴ 10
5
votes
15
replies
5.0k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 10 months ago by 65k • written 6.8 years ago by ▴ 10
1
vote
15
replies
8.0k
views
Exporting DESeq2 filtered results
DESeq2
updated 6 months ago by 65k • written 3.2 years ago by ▴ 10
8
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15
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1.4k
views
PCA percent variance DESeq2
PCA DESeq2
8 months ago • updated 7 months ago IUH • 0
4
votes
13
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1.3k
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Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
1
vote
13
replies
876
views
Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions replicates SmallRNAData DESeq2
updated 3 months ago by ★ 3.9k • written 4 months ago by ▴ 10
0
votes
13
replies
658
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2 SmallRNA
updated 8 weeks ago by 41k • written 8 weeks ago by • 0
9
votes
12
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7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 6 days ago by • 0 • written 8.8 years ago by ▴ 30
3
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12
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2.1k
views
t.test to determine the P-value in DESeq2
DESeq2
written 18 months ago by • 0
2
votes
12
replies
1.3k
views
P-value inflation?
DESeq2
updated 8 months ago by 65k • written 8 months ago by ▴ 10
1
vote
12
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2.7k
views
How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 6 months ago by ★ 1.5k • written 21 months ago by • 0
1
vote
12
replies
1.0k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
9 weeks ago • updated 8 weeks ago paria.alipour • 0
8
votes
12
replies
2.5k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by 41k • written 12 months ago by ▴ 90
1
vote
11
replies
989
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
6
votes
11
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3.9k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 6 weeks ago by • 0 • written 3.2 years ago by ▴ 40
6
votes
11
replies
26k
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With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 8 months ago by • 0 • written 9.2 years ago by ▴ 40
2
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10
replies
3.2k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 6 months ago by 41k • written 5.7 years ago by ▴ 20
2
votes
10
replies
1.1k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago • updated 5 months ago rohitsatyam102 ▴ 20
0
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9
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2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 5 months ago by • 0 • written 6.5 years ago by ▴ 60
0
votes
9
replies
1.4k
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Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin DESeq2
updated 6 months ago by ▴ 10 • written 21 months ago by ▴ 10
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
0
votes
9
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825
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DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
8 months ago mjd275 • 0
2
votes
9
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1.2k
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Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
9 months ago Ndimensional ▴ 20
4
votes
9
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1.2k
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RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
1
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9
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5.2k
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how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.1 years ago by • 0
1
vote
9
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863
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DESeq2 not replicable results
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
0
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9
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1.3k
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ranking the DeSeq2 results using t-values?
DESeq2
updated 10 months ago by 41k • written 10 months ago by ▴ 10
4
votes
9
replies
4.3k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 11 months ago by • 0 • written 6.8 years ago by • 0
8
votes
8
replies
9.7k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 7 months ago by • 0 • written 4.8 years ago by ▴ 40
1
vote
8
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1.2k
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DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 24 days ago by ★ 13k • written 9 months ago by ▴ 10
1
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8
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1.5k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 10 months ago by • 0
0
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8
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798
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
5 months ago Luca • 0
0
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8
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374
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 0
2
votes
8
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1.0k
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Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
10 months ago Ndimensional ▴ 20
1
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8
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2.7k
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Significantly regulated genes produced by only a few affected samples
deseq2
written 6.1 years ago by ▴ 60
1
vote
8
replies
2.5k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 4 months ago by • 0 • written 3.3 years ago by ▴ 10
0
votes
8
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701
views
Deseq2 Results are different using batch design
DESeq2
9 months ago hemantcnaik • 0
4
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8
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2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 16 months ago by ▴ 20
0
votes
8
replies
173
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 2 hours ago by ★ 1.3k • written 1 day ago by • 0
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 6 months ago by ▴ 10 • written 6.5 years ago by ▴ 30
4
votes
7
replies
838
views
weird volcano plot
DESeq2
updated 7 weeks ago by • 0 • written 5 months ago by ▴ 10
8
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7
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1.7k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 9 months ago by ▴ 20 • written 18 months ago by ▴ 20
0
votes
7
replies
385
views
DESeq filtering specific to contrasts
DESeq2
updated 5 days ago by 41k • written 9 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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