Showing : DESEQ2 • reset
3
votes
4
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1.7k
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DESeq2 with 2 biological replicates: if the replicates are not compatible for some genes
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
5
replies
1.5k
views
DESeq2 res remove some genes
deseq2 res
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 50
5
votes
4
replies
2.9k
views
DESeq2 question about use of DESeqDataSetFromTximport() from RSEM data
deseq2 software error
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
0
votes
5
replies
1.7k
views
DRIMSeq with technical replicates
DRIMSeq R DTU technical replicates deseq2
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
0
votes
3
replies
634
views
DESeq2 analysis : lots of NA results when adding covariables
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
1
reply
584
views
Can I use the default DESEQ2 normalization for samples with large differences in library early size
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
4
votes
5
replies
2.2k
views
Installing DESeq2 fails ; R can't find basic commands like 'rm' and 'mv'
deseq2 install software error
5.4 years ago mja18 ▴ 40
5
votes
3
replies
2.2k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 20
3
votes
2
replies
6.7k
views
DESeq2 design formula with multiple factors
deseq2 RNA-Seq
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
1
vote
2
replies
723
views
Can Wald's test be replaced with LRT
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
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1
reply
1.7k
views
How to input the TCGA HTseq-count matrix into DESeq2
deseq2 TCGA HTSeq-count
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
votes
8
replies
927
views
Deseq2 resultsNames() giving header instead of values
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
2
votes
3
replies
925
views
DESeq2 nested interaction and individual batch correction question
deseq2
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
3
votes
1
reply
1.6k
views
Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 180
0
votes
6
replies
8.3k
views
Issues installing DESeq2, installation path not writable, package: survival
deseq2 survival
updated 3.0 years ago by • 0 • written 5.4 years ago by • 0
1
vote
1
reply
1.2k
views
log2 fold change
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
1
vote
2
replies
632
views
Cannot install DeSeq on RStudio version 6.3.2
deseq2
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
0
votes
2
replies
918
views
Using mixed-model in differential expression analysis for bulk RNAseq
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
5
votes
7
replies
2.6k
views
tximeta - problem importing salmon files
tximeta deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
1
vote
5
replies
3.5k
views
Spearman correlation for RNA SEQ data
deseq2 rnaseq statistic
updated 5.4 years ago by ★ 3.4k • written 5.4 years ago by • 0
7
votes
6
replies
1.5k
views
Odd DESeq2 results - high significance in genes with too many zeros
deseq2 rna-seq
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
2
votes
2
replies
3.4k
views
DESeqDataSetFromTximport with and without offset
deseq2 tximport
5.4 years ago igor ▴ 50
0
votes
2
replies
2.7k
views
Error in taxa_are_rows(x) : trying to get slot "taxa_are_rows" from an object (class "otu_table") that is not an S4 object
deseq2 phyloseq
5.4 years ago jaiber.solano.i • 0
0
votes
1
reply
1.5k
views
DESeq2 normalization single cell
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 100
1
vote
6
replies
6.3k
views
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
deseq2 rownames
updated 4.2 years ago by 43k • written 5.4 years ago by ▴ 10
0
votes
3
replies
2.1k
views
SummarizedExperiement extract assay with no name
deseq2
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 10
0
votes
8
replies
1.2k
views
Deseq2 weird values for Log2FC and pvalue.
deseq2 rnaseq r
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
votes
2
replies
1.2k
views
mirna-mrna interation mircomb (from DEGs and DEMs lists)
deseq2 mircomb degs dems
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
0
votes
3
replies
863
views
DESeq2 Design Model and Results Function Set-Up - How to know if using the interaction term is appropriate?
deseq2 rnaseq
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
votes
1
reply
1.1k
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
1
vote
3
replies
739
views
MAplots after lfcshrink
DESeq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
2
votes
6
replies
1.9k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 5.4 years ago by ★ 29k • written 5.4 years ago by • 0
1
vote
1
reply
878
views
A question for clarification regarding counts input to DESeqDataSetFromMatrix
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 60
4
votes
6
replies
3.1k
views
Using spike-in RNA for normalization of Salmon counts imported using Tximport
deseq2 Tximport Sizefactors normalizationfactors spike-in
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
1
vote
2
replies
1.8k
views
"Error in nbinomLRT(... less than one degree of freedom"... Isolating main and interaction effects with the LRT?
deseq2 main effects interaction effects R lrt
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
4
votes
5
replies
1.7k
views
Custom Functional for automated DESeq2 running
deseq2
updated 5.4 years ago by ★ 1.4k • written 5.4 years ago by ▴ 20
0
votes
2
replies
2.3k
views
DESeq2 doubts about transformations + nbinomWaldtest warning
rna-seq deseq2 warnings nbinomWaldTest transformation
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
1
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1
reply
1.3k
views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2 apeglm
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
votes
7
replies
25k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
3
votes
9
replies
7.3k
views
DESeq2: Clarification on independent filtering threshold values
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 20
1
vote
1
reply
613
views
Unable to run tximport using sample.info ?
tximport deseq2 edgeR
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
5
votes
10
replies
2.0k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
4
votes
4
replies
8.2k
views
plotPCA in DESeq2
software error deseq2
5.4 years ago yueli7 ▴ 20
1
vote
3
replies
922
views
Use Tx2Gene for Annotation
deseq2 annotation r
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
7
votes
10
replies
3.0k
views
is there a function in edger the same as vst or rlog in deseq2
edger normalization deseq2
updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 20
2
votes
20
replies
4.1k
views
plotPCA in DESeq2
software error deseq2
5.4 years ago yueli7 ▴ 20
1
vote
5
replies
4.5k
views
Can't Download DESeq2 Package (Ubuntu 20.04; R 4.0.1; BioConductor 3.11)
deseq2 install r4.0 bioconductor3.11 ubuntu20.04
5.4 years ago ruwaa.ibrahem • 0
0
votes
7
replies
2.9k
views
Filter Out Low Read Counts
deseq2 r
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
votes
3
replies
641
views
What to do when two groups with untreated baseline show differentially expressed genes/taxa
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
1
vote
2
replies
4.5k
views
How to do correlation analysis using DESeq2?
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
4,839 results • Page 38 of 97
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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
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