Showing : DESeq2 • reset
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.1 years ago by ▴ 40
13
votes
22
replies
26k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 8 weeks ago by 41k • written 7.8 years ago by ▴ 30
6
votes
11
replies
26k
views
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
3
votes
6
replies
22k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 3 months ago by • 0 • written 5.6 years ago by • 0
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 8 months ago by • 0 • written 8.3 years ago by ▴ 60
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 12 months ago by ★ 4.0k • written 7.7 years ago by ▴ 20
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 6 months ago by • 0 • written 5.4 years ago by • 0
25
votes
7
replies
10k
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
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 4.7 years ago by ▴ 40
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
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 1 day ago by • 0 • written 8.8 years ago by ▴ 30
5
votes
18
replies
7.4k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 4 months ago by • 0 • written 2.2 years ago by • 0
1
vote
9
replies
5.2k
views
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
9
votes
5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 4 months ago by 50k • written 8.2 years ago by ▴ 90
5
votes
15
replies
4.9k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 10 months ago by 65k • written 6.8 years 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
6
votes
5
replies
4.1k
views
DESeq2: Extremely low pvalues
deseq2
updated 9 months ago by 65k • written 7.7 years ago by ▴ 20
2
votes
2
replies
4.1k
views
choosing the normalization method (rlog, variance stabilizing transformation)
variancestabilizingtransformation rlog transformation deseq2
updated 5 months ago by • 0 • written 6.4 years ago by ▴ 80
6
votes
11
replies
3.9k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 5 weeks ago by • 0 • written 3.1 years ago by ▴ 40
0
votes
17
replies
3.4k
views
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
2
votes
10
replies
3.1k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 6 months ago by 41k • written 5.7 years ago by ▴ 20
2
votes
6
replies
2.9k
views
DESeq2 Dispersion Per Condition
deseq2
updated 9 months ago by • 0 • written 8.0 years ago by ▴ 20
1
vote
2
replies
2.8k
views
TPM to raw counts
salmon DESeq2
updated 4 months ago by • 0 • written 2.3 years ago by • 0
7
votes
4
replies
2.7k
views
Normalized counts of DESeq2 affected by design formula?
deseq2
updated 3 months ago by • 0 • written 6.1 years ago by ▴ 20
3
votes
6
replies
2.7k
views
DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 8 weeks ago by • 0 • written 5.2 years ago by ▴ 50
1
vote
8
replies
2.7k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.1 years ago by ▴ 60
1
vote
12
replies
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
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
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 11 months ago by ▴ 90
0
votes
9
replies
2.4k
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
2
replies
2.2k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 7 months ago by • 0 • written 2.0 years ago by • 0
4
votes
6
replies
2.2k
views
DESeq2 for single cell pseudobulk processing
DESeq2
updated 11 months ago by 41k • written 12 months ago by • 0
5
votes
14
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 9 hours ago by • 0 • written 4.6 years ago by ▴ 10
3
votes
16
replies
2.1k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 12 weeks ago by 3.8k • written 2.8 years ago by ▴ 10
4
votes
8
replies
2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 10 months ago by 50k • written 16 months ago by ▴ 20
3
votes
12
replies
2.1k
views
t.test to determine the P-value in DESeq2
DESeq2
written 18 months ago by • 0
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.3 years ago by ▴ 10
2
votes
2
replies
2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 8 months ago by • 0 • written 6.3 years ago by • 0
0
votes
5
replies
1.9k
views
DESeq LRT test and construction of Co-expression network
LRT co-expression network deseq2 time course experiment network analysis
updated 10 months ago by • 0 • written 6.1 years ago by ▴ 30
2
votes
7
replies
1.8k
views
optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 11 months ago by 41k • written 11 months ago by ★ 4.0k
1
vote
3
replies
1.7k
views
DeSEQ 2 Error: some values in assay are negative
Countmatrix negativeassay DESeq2
10 months ago dania.khalid • 0
8
votes
7
replies
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
1
vote
3
replies
1.7k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 4.1 years ago by • 0
2
votes
17
replies
1.7k
views
lfcshrink error DESeq2
DESeq2 lfcshrink DESe
updated 11 months ago by 41k • written 11 months ago by • 0
0
votes
7
replies
1.5k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
1
vote
8
replies
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
votes
6
replies
1.5k
views
deseq2 pre filter rna seq
deseq2 rnaseq
updated 6 months ago by 41k • written 4.8 years ago by • 0
1
vote
5
replies
1.4k
views
How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
12 months ago • updated 11 months ago Weiqian ▴ 10
1
vote
1
reply
1.4k
views
News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 5.2 years ago by 1.6k
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 11 months ago by • 0 • written 5.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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Popular Question to James W. MacDonald 65k
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Scholar to Peter Hickey ▴ 740
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