Showing : DESEq2 • reset
1
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unable to install DESeq2 there is no package called XML
deseq2 bioconductor windows xml installation
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
3
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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
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5
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1.6k
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DESeq2 res remove some genes
deseq2 res
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 50
5
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4
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2.9k
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DESeq2 question about use of DESeqDataSetFromTximport() from RSEM data
deseq2 software error
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
0
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5
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1.7k
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DRIMSeq with technical replicates
DRIMSeq R DTU technical replicates deseq2
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
0
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3
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635
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DESeq2 analysis : lots of NA results when adding covariables
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
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1
reply
592
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Can I use the default DESEQ2 normalization for samples with large differences in library early size
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
4
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5
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2.2k
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Installing DESeq2 fails ; R can't find basic commands like 'rm' and 'mv'
deseq2 install software error
5.4 years ago mja18 ▴ 40
5
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3
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2.2k
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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
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2
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6.7k
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DESeq2 design formula with multiple factors
deseq2 RNA-Seq
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
1
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2
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730
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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
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1.7k
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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
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8
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940
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Deseq2 resultsNames() giving header instead of values
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
2
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3
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928
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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
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1
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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
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6
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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
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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
637
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
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2
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933
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
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7
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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
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5
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3.5k
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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
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6
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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
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2
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3.4k
views
DESeqDataSetFromTximport with and without offset
deseq2 tximport
5.4 years ago igor ▴ 50
0
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2
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2.7k
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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
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1
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1.5k
views
DESeq2 normalization single cell
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 100
1
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6
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6.4k
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
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3
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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
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8
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1.3k
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
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2
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1.2k
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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
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3
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870
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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
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1
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1.1k
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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
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3
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743
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MAplots after lfcshrink
DESeq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
2
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6
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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
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1
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882
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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
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6
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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
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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
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5
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1.8k
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Custom Functional for automated DESeq2 running
deseq2
updated 5.4 years ago by ★ 1.4k • written 5.4 years ago by ▴ 20
0
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2
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2.3k
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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
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1.3k
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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
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7
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25k
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DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
3
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9
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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
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1
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616
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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
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10
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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
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4
replies
8.2k
views
plotPCA in DESeq2
software error deseq2
5.4 years ago yueli7 ▴ 20
1
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3
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929
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Use Tx2Gene for Annotation
deseq2 annotation r
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
7
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10
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3.0k
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is there a function in edger the same as vst or rlog in deseq2
edger normalization deseq2
updated 5.5 years ago by 53k • written 5.5 years ago by ▴ 20
2
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20
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4.1k
views
plotPCA in DESeq2
software error deseq2
5.5 years ago yueli7 ▴ 20
1
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5
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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
5.5 years ago ruwaa.ibrahem • 0
0
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7
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2.9k
views
Filter Out Low Read Counts
deseq2 r
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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3
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647
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What to do when two groups with untreated baseline show differentially expressed genes/taxa
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
4,840 results • Page 38 of 97
Recent ...
Replies
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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