Showing : DESEQ2 • reset
2
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1.7k
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Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
DESeq2 tpm Normalization
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
2
replies
1.8k
views
Deseq2 outlier detection (about Cook's distance)
DESeq2 RNASeq DifferentialExpression
4.3 years ago peter.zhouyu • 0
0
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4
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2.2k
views
Batch-corrected expression matrix NOT on a log2 scale
DESeq2 limma
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 70
0
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5
replies
1.1k
views
Incosistency between contrast and coef parameters in lfcShrink function
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
3
votes
1
reply
1.3k
views
Compare two samples by Deseqs
DESeq2 RNASeq
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 10
0
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2
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966
views
DESEQ2 - compensating quality difference in replicate samples
DESeq2
4.3 years ago Shail • 0
0
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1
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1.4k
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Subject paired DESeq2 design
DESeq2 paired design
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 10
0
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2
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2.1k
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Relative abundance of differentially abundant ASVs after DESeq2
DESeq2
4.3 years ago Marion • 0
0
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4
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2.7k
views
DESeq2::DESeq(..., parallel = TRUE) fails if a partition has only genes with 0 counts across all samples
DESeq2 BiocParallel
4.3 years ago Steffi Grote ▴ 10
0
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3
replies
1.6k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
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2
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896
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Paired samples analysis
DESeq2
4.3 years ago Hanan • 0
2
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6
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4.4k
views
DESeq2 - understanding intercept and contrasts
DESeq2 RNASeq
4.3 years ago sarah-spie ▴ 20
0
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2
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769
views
Interaction terms and selection of coef in normal and shrunk results
DESeq2
4.3 years ago Richelle • 0
0
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1
reply
739
views
DESeq2, what to do when controls are 7 times more abundant than treatments
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
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2
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1.6k
views
Warning message of NAs introduced by coercion after nbinomWaldTest
DESeq2
4.3 years ago Richelle • 0
0
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1
reply
1.4k
views
log2 fold change calculation in deseq2.
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
5
votes
8
replies
4.3k
views
Combat and dds Object
DESeq2 combat
updated 2.8 years ago by ★ 5.0k • written 4.3 years ago by ▴ 50
1
vote
2
replies
1.4k
views
What lfcSE is dependent upon?
DESeq2
written 4.3 years ago by ▴ 10
4
votes
2
replies
1.2k
views
P value and Adj. P value showing N/A
DESeq2
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by • 0
2
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2
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2.1k
views
DESeq2 Shrinkage methods for scRNA-Seq
DESeq2
4.3 years ago Pedro Tan ▴ 10
0
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1
reply
1.5k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
4.3 years ago slcno • 0
0
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1
reply
1.1k
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 4.3 years ago by 43k • written 4.4 years ago by • 0
0
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2
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1.4k
views
Using DESEQ2 with selective gene vs all genes
DESeq2
4.3 years ago Shail • 0
2
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2
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1.6k
views
batch effect and size factor differences: vst vs. rlog
DESeq2
4.3 years ago Hannah • 0
0
votes
1
reply
602
views
DESeq2 - correct for nested batch with NA values?
DESeq2 deseq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
2
votes
3
replies
2.0k
views
vst of DESeq2 for bulk UMI counts
DESeq2 normaliz Normalization
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
2
votes
1
reply
1.0k
views
Why does samples order subtly influence the results of DESeq2?
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 10
2
votes
13
replies
3.6k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
4.3 years ago RDoc ▴ 10
3
votes
2
replies
1.9k
views
DESeq2, geometric means using posCounts
DESeq2
4.3 years ago Phil ▴ 10
1
vote
1
reply
1.6k
views
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
DESeq2 Diffbind
updated 4.3 years ago by ★ 5.2k • written 4.4 years ago by ▴ 10
3
votes
4
replies
1.9k
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2 DRIMSeq dtu RNASeq
4.4 years ago • updated 4.3 years ago sbcn ▴ 80
0
votes
6
replies
2.3k
views
Differential Expression analysis of specific list of genes
DESeq2
updated 4.3 years ago by ★ 13k • written 4.4 years ago by ▴ 10
0
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2
replies
1.6k
views
genefilter not available for R v4.1/arm64
DESeq2 genefilter
4.4 years ago • updated 4.3 years ago jeremymsimon ▴ 20
0
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11
replies
1.9k
views
Deseq paired samples
DESeq2
updated 4.3 years ago by 43k • written 4.4 years ago by ▴ 10
1
vote
5
replies
4.6k
views
Problem with DESeq2 installation using in R 1.4.1717
DESeq2 Problem installation with
updated 4.4 years ago by ▴ 760 • written 4.4 years ago by • 0
0
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4
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1.3k
views
Problems with pulling specific variables
DESeq2
4.4 years ago Bine ▴ 50
0
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2
replies
1.9k
views
DeSEq2-- error- count matrix
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
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3
replies
1.4k
views
tximport fails when RSEM output options produce files with additional columns?
DESeq2 tximportData tximpor
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
5
votes
5
replies
1.7k
views
Idea: Using DESeq2 to test a change in ratio of two genes
DESeq2
updated 4.3 years ago by 43k • written 4.4 years ago by ▴ 20
0
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5
replies
9.4k
views
error in relevel.default - 'relevel' only for (unordered) factors when setting baseline
DESeq2
4.4 years ago Yihan • 0
0
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1
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1.2k
views
confusion about Deseq2 wording in the vignette ( additive model with main effects only vs interaction )
DESeq2
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 10
3
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2
replies
3.7k
views
A permanent error in DESeq2
DESeq2
4.4 years ago AZ ▴ 30
0
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1
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1.8k
views
DESeq2 Paired Analysis--Tumor vs Normal
DESeq2
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
2
votes
3
replies
1.6k
views
The P-values with lfcShrink and ashr shrinkage estimator
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
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1
reply
795
views
Identifying sample considered in each group
DESeq2
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
0
votes
1
reply
902
views
Group-specific condition effect
DESeq2
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
0
votes
1
reply
933
views
samples did not decently separate via pcaPlot
pcaplot deseq2
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
0
votes
20
replies
3.7k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2 DEGs
4.4 years ago • updated 4.3 years ago Ming ▴ 380
1
vote
6
replies
3.4k
views
deseq2 for TCGA tumor/normal paired sample from multiple patients
deseq2
updated 4.4 years ago by 43k • written 10.0 years ago by • 0
1
vote
5
replies
3.9k
views
undefined columns selected
DESeq2
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
4,839 results • Page 28 of 97
Recent ...
Replies
Comment: Post translational modifications and phosphoproteomics in limpa? by james.eapen • 0
Thank you!
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by ATpoint ★ 5.0k
The donor effect is crystal clear, and absent in these suspicious samples. It strongly argues for a technical problem. If you really need s…
Answer: mzR-Rcpp compiler version issue by Laurent Gatto 1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co by jamie.gearing ▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Votes
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
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