Showing : DEseq2 • reset
2
votes
1
reply
733
views
rlog in reference level
deseq2
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by ▴ 10
1
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2
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1.4k
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Does DESeq2 need to correct for overlapping regions?
deseq2 ihw
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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4
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1.9k
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DESeq2 unpaired RNAseq analysis
deseq2 rnaseq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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8
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3.3k
views
DESeq2 lfcShrink warning use ashr method
deseq2
6.2 years ago MatthewP • 0
0
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2
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1.5k
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2 DEXSeq BioCParallel
updated 6.2 years ago by ★ 1.9k • written 6.2 years ago by • 0
1
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5
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1.2k
views
Switching RNAseq count data to explanatory variable?
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
1
vote
5
replies
1.9k
views
DESeq2: Normalization of allele specific counts in RNA-seq
deseq2 rnaseq allele-specific normalization
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 20
0
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1
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2.1k
views
Different Expression Analysis with EDASeq,DESeq2,edgeR,RUVSeq
deseq2 normalization RUVg edger
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
2
votes
3
replies
1.6k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 6.3 years ago by ★ 1.4k • written 6.3 years ago by ▴ 80
2
votes
2
replies
1.6k
views
DEseq2 resultsNames doesn not reproduce the right comparisons
deseq2 resultsNames()
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
1
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1
reply
1.2k
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 30
0
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2
replies
987
views
DESeq2 design matrix choice
deseq2 design matrix
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
votes
6
replies
3.3k
views
Removing Batch effect on the raw counts or normalised counts
DEseq2 batch effect RNAseq
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 30
3
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2
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1.5k
views
DESeq2 for big data sets
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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2
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1.9k
views
DESeq2 installs but then can't be brought in as a library
deseq2 R3.6.1 library(DESeq2)
updated 3.1 years ago by • 0 • written 6.3 years ago by • 0
2
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2
replies
1.6k
views
DESeq2 error due to zeros
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 20
0
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2
replies
1.7k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
2
votes
1
reply
2.9k
views
DESeq2 heatmap and rlog transformed values
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
0
votes
5
replies
1.0k
views
Phyloseq to DESeq2 Help
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
5
votes
7
replies
12k
views
Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by ▴ 10
2
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2
replies
1.4k
views
DESeq2 s-value threshold for FSOS events
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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1
reply
805
views
DESeq2 Wald test p-values
deseq2
6.3 years ago Homer • 0
0
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1
reply
2.4k
views
package DESeqDataSet is not available for R version 3.6.1
deseq2
updated 6.3 years ago by 25k • written 6.3 years ago by • 0
0
votes
2
replies
781
views
DESeq2: Paired multifactor test with batch effect - one or more variables in design formula are linear combinations of others
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 60
0
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2
replies
788
views
DESeq2 rlog as the input for ARACNE
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Using VST normalized values for "external" single gene analysis
VST normalization deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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1
reply
602
views
Question about design formulas in DESeq2 (4 genotypes, 2 batches, 2 cell states)
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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11
replies
1.9k
views
tx2gene for xenopus LAEVIS
deseq2
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
5
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13
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4.1k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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1
reply
1.6k
views
timing when to use collapseReplicates in DESeq2
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
1
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1
reply
1.2k
views
samples.txt?how to generate
deseq2
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
2
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4
replies
1.9k
views
DESeq2--compare two log2-transformed fold changes in paired and multi factor sample
deseq2
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by ▴ 10
0
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1
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441
views
how raw data is processed after estimation of mean-variation relation?
normalization deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
votes
2
replies
951
views
Reads with ambiguous annotation
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 60
0
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1
reply
386
views
Identifying unique DEG and synergistically affected genes in a combination treatment (DESeq2)
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
1
vote
2
replies
2.9k
views
How can I delete specific rows (using gene name) from a DESeq2 dataset (or even just a counts file.
deseq2
updated 6.3 years ago by ★ 13k • written 6.3 years ago by • 0
0
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5
replies
1.8k
views
EnsemblGene ID conversion
deseq2 annotation Tutorial
updated 6.3 years ago by 25k • written 6.3 years ago by • 0
0
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1
reply
595
views
about DESeq2 analysis on time series data
deseq2
6.3 years ago Cindy • 0
0
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1
reply
452
views
Sai Nikhith Cholleti
edger deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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1
reply
1.2k
views
DESeq2 - Comparing RNA-Seq and Ribo-Seq
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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4
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1.3k
views
DEseq2 analysis time-series data under two conditions
deseq2
6.3 years ago Cindy • 0
22
votes
12
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31k
views
New function lfcShrink() in DESeq2
deseq2
updated 6.3 years ago by • 0 • written 8.6 years ago by 43k
0
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8
replies
2.9k
views
Two controls in RNAseq formula for DESeq2
deseq2 formula controls design
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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2
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4.3k
views
DESeq2: How to correct for multiple comparisons
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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6
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2.4k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by ▴ 670
8
votes
5
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5.4k
views
the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
normalization DESeq2 edgeR
updated 6.3 years ago by 53k • written 6.3 years ago by ▴ 10
4
votes
8
replies
26k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 20
0
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1
reply
769
views
DESeq2 question about design formula with nested variables
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
votes
8
replies
1.3k
views
Suggestions for avoiding False Positives while identifying differentially expressed genes with more than 3 samples per group
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
7
votes
4
replies
3.1k
views
RNA-seq normalization without filtering
deseq2 edger normalization RNAseq
updated 6.3 years ago by ★ 13k • written 6.3 years ago by ▴ 50
4,840 results • Page 47 of 97
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
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.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
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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