Showing : DESEQ2 • reset
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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1.8k
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DESeq2 unpaired RNAseq analysis
deseq2 rnaseq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
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8
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3.3k
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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
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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
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Switching RNAseq count data to explanatory variable?
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
1
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5
replies
1.9k
views
DESeq2: Normalization of allele specific counts in RNA-seq
deseq2 rnaseq allele-specific normalization
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 20
0
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1
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2.1k
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Different Expression Analysis with EDASeq,DESeq2,edgeR,RUVSeq
deseq2 normalization RUVg edger
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
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3
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1.6k
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Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by ▴ 80
2
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2
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1.6k
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DEseq2 resultsNames doesn not reproduce the right comparisons
deseq2 resultsNames()
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
1
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1
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1.1k
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DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 30
0
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2
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983
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DESeq2 design matrix choice
deseq2 design matrix
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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6
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3.3k
views
Removing Batch effect on the raw counts or normalised counts
DEseq2 batch effect RNAseq
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 30
3
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2
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1.5k
views
DESeq2 for big data sets
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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2
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1.9k
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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 6.2 years ago by • 0
2
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2
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1.6k
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DESeq2 error due to zeros
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 20
0
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2
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1.7k
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Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
votes
1
reply
2.9k
views
DESeq2 heatmap and rlog transformed values
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
0
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5
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1.0k
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Phyloseq to DESeq2 Help
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
5
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7
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12k
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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
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1.3k
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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
801
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DESeq2 Wald test p-values
deseq2
6.3 years ago Homer • 0
0
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1
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2.4k
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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
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2
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776
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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
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786
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DESeq2 rlog as the input for ARACNE
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
0
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1
reply
1.4k
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
598
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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
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1.9k
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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
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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
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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
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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
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1.9k
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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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436
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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
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2
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940
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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
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381
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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
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2
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2.9k
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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
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1.8k
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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
592
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about DESeq2 analysis on time series data
deseq2
6.3 years ago Cindy • 0
0
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1
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451
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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
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1.2k
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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
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DEseq2 analysis time-series data under two conditions
deseq2
6.3 years ago Cindy • 0
22
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12
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31k
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New function lfcShrink() in DESeq2
deseq2
updated 6.3 years ago by • 0 • written 8.5 years ago by 43k
0
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8
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2.9k
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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
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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
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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
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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
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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
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767
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DESeq2 question about design formula with nested variables
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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8
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1.3k
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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
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4
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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
0
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0
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936
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News: Course in Berlin- Genomics with R and Bioconductor - September 16-20
deseq2 edger limma News
6.3 years ago info ▴ 10
4,839 results • Page 47 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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