Showing : RnaSeq • reset
1
vote
4
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293
views
Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
5 days ago • updated 4 days ago Mariami • 0
0
votes
5
replies
282
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 18 days ago by 43k • written 18 days ago by • 0
3
votes
4
replies
413
views
Question about the filterByExpr function inputs in edgeR
RNASeq filter design edgeR model.matrix
4 weeks ago mohammedtoufiq91 ▴ 10
8
votes
8
replies
3.0k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
written 7.4 years ago by ▴ 20
0
votes
0
replies
132
views
Job: Job:Computational Biologist position at the University of Alabama at Birmingham
hiring RNASeq JobPosting SingleCell SpatialData
5 weeks ago lianov • 0
3
votes
6
replies
1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 12 weeks ago by • 0
0
votes
2
replies
583
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 10 weeks ago by • 0 • written 5 months ago by • 0
0
votes
1
reply
283
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
5
votes
13
replies
1.6k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 months ago by 53k • written 5 months ago by • 0
0
votes
1
reply
3.3k
views
Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 11.3 years ago by • 0
2
votes
9
replies
1.1k
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
6 months ago mohammedtoufiq91 ▴ 10
0
votes
8
replies
740
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago Jiahao Tian • 0
3
votes
13
replies
2.4k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
3
votes
2
replies
1.1k
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
6 months ago mohammedtoufiq91 ▴ 10
0
votes
5
replies
1.1k
views
WGCNA
WGCNA Normalization RNASeq
written 12 months ago by • 0
3
votes
2
replies
1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
0
votes
1
reply
675
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 8 months ago by 43k • written 9 months ago by • 0
2
votes
5
replies
1.9k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 8 months ago by ▴ 110 • written 8 months ago by ▴ 10
0
votes
0
replies
392
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
9 months ago dudwnsrla1 • 0
4
votes
7
replies
3.6k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
9 months ago • updated 4 months ago massimo ▴ 10
1
vote
1
reply
1.4k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
votes
4
replies
1.6k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 11 months ago by • 0
0
votes
0
replies
722
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
11 months ago GT • 0
0
votes
3
replies
1.2k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 12 months ago by • 0
1
vote
8
replies
2.9k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 15 months ago by • 0
3
votes
7
replies
2.1k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
24 months ago • updated 5 months ago boczniak767 ▴ 740
12
votes
5
replies
5.6k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 8 months ago by • 0 • written 2.2 years ago by • 0
8
votes
10
replies
18k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 9 months ago by ★ 5.0k • written 9.5 years ago by ▴ 20
0
votes
3
replies
1.5k
views
PCA subset of genes vs DE
DESeq2 RNASeq
written 3.0 years ago by ▴ 20
2
votes
4
replies
2.6k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 11 months ago by 43k • written 3.7 years ago by ▴ 10
0
votes
2
replies
1.4k
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq splicing RNAseq DEXSeq
written 6.2 years ago by ▴ 10
1
vote
3
replies
6.6k
views
Log2 fold change value in DESeq2
deseq2 rnaseq
written 8.3 years ago by • 0
9
votes
12
replies
11k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
written 9.7 years ago by ▴ 20
3
votes
5
replies
5.5k
views
plotMDS in edgeR
edger rnaseq
written 10.4 years ago by ▴ 30
3
votes
5
replies
2.0k
views
weird model design for DE analysis
RNASeq
updated 6 months ago by 53k • written 12.6 years ago by ▴ 140
35 results • Page 1 of 1
Recent ...
Replies
Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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