Showing : DESEQ2 • reset
2
votes
2
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2.2k
views
subsetting VST counts from one dataset
deseq2 rna-seq
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 60
8
votes
8
replies
2.0k
views
DESeq2 rlog blinding if calculating variance of expression?
deseq2 rlog
5.6 years ago Zach Roe ▴ 10
0
votes
1
reply
1.6k
views
DESeq2 and Heatmap for multiple conditions
deseq2 normalization
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 20
0
votes
1
reply
1.4k
views
Deseq2 how to get input data for plotCounts for a single gene
deseq2 plotcounts
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
4
votes
7
replies
4.8k
views
ControlGenes/ housekeeping genes Deseq2
normalization deseq2 sizefactors
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 40
3
votes
4
replies
2.1k
views
Massive L2FC in DESeq2
deseq2 ashr rna-seq
5.6 years ago Alex • 0
6
votes
7
replies
6.0k
views
Converting numeric variables to factors in DESeq metadata
deseq2
updated 3.4 years ago by • 0 • written 5.6 years ago by • 0
5
votes
5
replies
3.9k
views
Cannot extract size factor from DESeq2 analysis
deseq2 tximport
updated 5 months ago by 43k • written 5.6 years ago by • 0
1
vote
1
reply
1.2k
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
2
replies
1.1k
views
GO analysis without gene IDs?
deseq2 annotation go
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 60
6
votes
14
replies
22k
views
having trouble formatting data for DE analysis
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
4
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5
replies
3.6k
views
How to plot the batch corrected values in DESeq2
deseq2 normalization
updated 4.3 years ago by 43k • written 6.9 years ago by • 0
0
votes
1
reply
940
views
DESeq2 multiple testing handling
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
1
reply
3.5k
views
Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
5.6 years ago cupret • 0
0
votes
5
replies
3.0k
views
Deseq2, lfcThreshold .
ashr Deseq2 lfcThreshold
updated 4.1 years ago by 43k • written 5.6 years ago by • 0
1
vote
2
replies
1.7k
views
DESeq2 runs slower in parallel than non-parallel mode, or it is stuck
deseq2
updated 5.6 years ago by ▴ 170 • written 5.6 years ago by ▴ 10
1
vote
1
reply
637
views
dds,listc() vs dds(,contrast=list c()
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 30
2
votes
2
replies
835
views
Placing groups in one or in different DESeq2 objects
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
17
replies
3.9k
views
DESeq2 shrunken log fold changes
deseq2
5.6 years ago dequattro.concetta ▴ 10
3
votes
3
replies
2.9k
views
Best way to include RIN in differential expression design
deseq2 limma
updated 5.6 years ago by ★ 3.4k • written 5.6 years ago by ▴ 180
2
votes
4
replies
2.0k
views
how to deal with the replicate count when do k-means or someother machine-learning
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 40
2
votes
2
replies
633
views
DESeq2 question: contrast to reflect treatment effect corrected by baseline
deseq2
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by ▴ 10
2
votes
6
replies
2.7k
views
Possible factor-related error message bug in DESeq2
deseq2
5.6 years ago thadryan • 0
1
vote
4
replies
962
views
Problem with batches and "Model matrix not full rank" during differential gene expression analysis with DESeq2
deseq2
updated 5.6 years ago by ★ 1.4k • written 5.6 years ago by • 0
0
votes
2
replies
1.3k
views
DESeq2/EdgeR for differential binding analaysis after RepEnrich2
deseq2 edgeR repenrich2 normalization
5.6 years ago mkmwong • 0
0
votes
2
replies
848
views
tx2gene for arabidopsis thaliana
deseq2
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
1
vote
2
replies
1.2k
views
Time-series analysis with control and treated samples, and Fold Change extraction in DESeq2
deseq2 time-serie time-course fold-change
updated 5.6 years ago by ★ 1.4k • written 5.6 years ago by • 0
3
votes
5
replies
14k
views
DESeq2 vs edgeR results analysis
deseq2 edgeR
updated 3.8 years ago by 53k • written 5.6 years ago by ▴ 40
1
vote
4
replies
2.3k
views
Data Structure for Read Count Analysis by DESeq2
deseq2 software error
updated 5.6 years ago by ★ 1.4k • written 5.6 years ago by ▴ 20
0
votes
1
reply
698
views
DESeq2 error multifactiorial design
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
1
vote
2
replies
704
views
A gene is only expressed in one sample, and DESeq2 counts it as a DEG. Is this reasonable? How to deal with individual differences?
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
1
vote
2
replies
873
views
Data Structure for Read Count Analysis by DESeq2
deseq2 software error
updated 5.6 years ago by ▴ 10 • written 5.6 years ago by ▴ 20
0
votes
1
reply
806
views
deseq2 for enrichments between different subcellular fractions?
deseq2 galaxy
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
4
replies
2.1k
views
Error package or namespace load failed for DESeq2
deseq2
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
0
votes
1
reply
776
views
Having issues generating manhattan plot in deseq2
deseq2 RNA-seq
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
5
replies
3.4k
views
Using raw pvalue instead of adjusted pvalue in Deseq 2
DESeq2 RNA-seq
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
3
replies
698
views
Unbalanced design and large difference in number of input reads for DESeq2
deseq2 normalization
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
8
replies
2.1k
views
Weird MA-plot (DESeq2)
deseq2 RNAseq
5.6 years ago jgarces • 0
0
votes
11
replies
2.3k
views
DESeq2 contrast and complex comparisons
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 100
0
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1
reply
1.3k
views
3x2 factorial design
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 30
0
votes
7
replies
1.1k
views
Highly differentially expressed genes having zero expression in one of the conditions lose significance if batch is added to the model in DESeq2
deseq2
5.6 years ago leonfodoulian • 0
0
votes
2
replies
1.6k
views
Error in DESeqDataSet: variables and colnames don't match when they do
deseq2 normalization
updated 5.6 years ago by • 0 • written 5.6 years ago by • 0
0
votes
1
reply
3.8k
views
DESeq2 with continuous variable
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
1
reply
301
views
issue with resultsNames and contrast function
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
2
votes
4
replies
3.0k
views
DESeq2 Error: package or namespace load failed for 'DESeq2'
RNA-Seq DESeq2
updated 5.6 years ago by ▴ 50 • written 5.6 years ago by ▴ 10
3
votes
5
replies
2.2k
views
Different numbers of DE genes using edgeR and DESEQ2
edger deseq2 rnaseq de
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 60
0
votes
10
replies
1.5k
views
Java & DESeq2
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 20
1
vote
11
replies
3.3k
views
Error uploading deseq2
deseq2 S4Vectors
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
1
vote
2
replies
825
views
trans-effect analysis with DESeq2
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
2
replies
3.6k
views
How to use DESeqDataSetFromHTSeqCount
deseq2
updated 5.6 years ago by ★ 1.4k • written 5.6 years ago by ▴ 20
4,839 results • Page 40 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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