Showing : DESeq2 • reset
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 3 months ago by 42k • written 7.9 years ago by ▴ 30
28
votes
21
replies
49k
views
deseq2 filter the low counts
deseq2 lowcount
updated 4 months ago by • 0 • written 9.3 years ago by ▴ 40
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 29 days ago by • 0 • written 4.7 years ago by ▴ 10
5
votes
18
replies
7.6k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 5 months ago by • 0 • written 2.3 years ago by • 0
0
votes
17
replies
3.5k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 11 months ago by • 0 • written 6.7 years ago by • 0
3
votes
16
replies
2.2k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 4 months ago by 3.9k • written 2.9 years ago by ▴ 10
8
votes
15
replies
1.6k
views
PCA percent variance DESeq2
PCA DESeq2
9 months ago IUH • 0
1
vote
15
replies
8.4k
views
Exporting DESeq2 filtered results
DESeq2
updated 7 months ago by 66k • written 3.3 years ago by ▴ 10
5
votes
15
replies
5.1k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 11 months ago by 66k • written 6.9 years ago by ▴ 10
1
vote
13
replies
985
views
Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions replicates SmallRNAData DESeq2
updated 4 months ago by ★ 3.9k • written 5 months ago by ▴ 10
4
votes
13
replies
1.5k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 8 months ago by 42k • written 9 months ago by • 0
0
votes
13
replies
752
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2 SmallRNA
updated 3 months ago by 42k • written 3 months ago by • 0
1
vote
12
replies
1.1k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
3 months ago paria.alipour • 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 weeks ago by • 0 • written 8.9 years ago by ▴ 30
2
votes
12
replies
1.4k
views
P-value inflation?
DESeq2
updated 9 months ago by 66k • written 9 months ago by ▴ 10
3
votes
12
replies
2.2k
views
t.test to determine the P-value in DESeq2
DESeq2
written 19 months ago by • 0
1
vote
12
replies
2.9k
views
How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 7 months ago by ★ 1.5k • written 22 months ago by • 0
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
6
votes
11
replies
4.1k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 11 weeks ago by • 0 • written 3.3 years ago by ▴ 40
0
votes
11
replies
1.4k
views
Unable to install DESeq2
DESeq2
updated 10 months ago by 66k • written 10 months ago by • 0
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 10 months ago by • 0 • written 9.3 years ago by ▴ 40
2
votes
10
replies
1.2k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
7 months ago • updated 6 months ago rohitsatyam102 ▴ 20
2
votes
10
replies
3.3k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 7 months ago by 42k • written 5.8 years ago by ▴ 20
4
votes
9
replies
1.2k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago Luca • 0
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 6 months ago by • 0 • written 6.6 years ago by ▴ 60
2
votes
9
replies
465
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 4 weeks ago by 66k • written 4 weeks ago by • 0
0
votes
9
replies
882
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
9 months ago mjd275 • 0
4
votes
9
replies
345
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 13 days ago by ★ 4.2k • written 15 days ago by • 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
11 months ago • updated 10 months ago Ndimensional ▴ 20
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
10 months ago Luca • 0
1
vote
9
replies
919
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
0
votes
9
replies
1.5k
views
ranking the DeSeq2 results using t-values?
DESeq2
updated 11 months ago by 42k • written 11 months ago by ▴ 10
0
votes
9
replies
1.5k
views
Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin DESeq2
updated 7 months ago by ▴ 10 • written 22 months ago by ▴ 10
8
votes
8
replies
10.0k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 8 months ago by • 0 • written 4.8 years ago by ▴ 40
0
votes
8
replies
431
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 5 weeks ago by ★ 1.4k • written 5 weeks ago by • 0
0
votes
8
replies
474
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
12 weeks ago • updated 11 weeks ago michelafrancesconi8 • 0
1
vote
8
replies
1.7k
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 11 months ago by • 0
0
votes
8
replies
855
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
7 months ago • updated 6 months ago Luca • 0
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
11 months ago Ndimensional ▴ 20
1
vote
8
replies
2.7k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 5 months ago by • 0 • written 3.4 years ago by ▴ 10
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by ▴ 60
1
vote
8
replies
1.4k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 8 weeks ago by ★ 13k • written 11 months ago by ▴ 10
0
votes
8
replies
754
views
Deseq2 Results are different using batch design
DESeq2
10 months ago hemantcnaik • 0
1
vote
8
replies
203
views
Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
7 days ago boczniak767 ▴ 720
0
votes
8
replies
590
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 15 days ago by ▴ 30 • written 16 days ago by • 0
0
votes
7
replies
480
views
DESeq2 filtering vs edgeR filtering
DESeq2
11 weeks ago • updated 9 weeks ago fr8712ca-s • 0
4
votes
7
replies
930
views
weird volcano plot
DESeq2
updated 12 weeks ago by • 0 • written 6 months ago by ▴ 10
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 7 months ago by ▴ 10 • written 6.6 years ago by ▴ 30
0
votes
7
replies
471
views
DESeq filtering specific to contrasts
DESeq2
updated 5 weeks ago by 42k • written 3 months ago by • 0
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 4 months ago by 50k • written 14 months ago by • 0
50 results • Page 1 of 1
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Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
The source script of the C function is available, just take it and compile the longestConsecutive function yourself, that's the easiest I g…
Comment: How to run allelic imbalance in apeglm by parayod376 • 0
Which I care about. [Papa's games][1] thank you for sharing the information. [1]: https://papasgamesfree.github.io
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!
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If you have functions in another R document, you have to `source` that document to load the functions into your workspace. Just like you wo…
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Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
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