Showing : rnaseq • reset
1
vote
4
replies
335
views
Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
14 days ago Mariami • 0
0
votes
5
replies
298
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 27 days ago by 43k • written 28 days ago by • 0
3
votes
4
replies
449
views
Question about the filterByExpr function inputs in edgeR
RNASeq filter design edgeR model.matrix
5 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 7.5 years ago by ▴ 20
0
votes
0
replies
147
views
Job: Job:Computational Biologist position at the University of Alabama at Birmingham
hiring RNASeq JobPosting SingleCell SpatialData
7 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 3 months ago by • 0
0
votes
2
replies
623
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 12 weeks ago by • 0 • written 5 months ago by • 0
0
votes
1
reply
290
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
1.7k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 5 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
1.2k
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
756
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
1.2k
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
7 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
686
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 9 months ago by 43k • written 9 months ago by • 0
2
votes
5
replies
2.0k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 9 months ago by ▴ 110 • written 9 months ago by ▴ 10
0
votes
0
replies
404
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
10 months ago • updated 4 months ago massimo ▴ 10
1
vote
1
reply
1.5k
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
781
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
11 months ago GT • 0
1
vote
8
replies
3.0k
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
2.2k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
2.0 years ago • updated 5 months ago boczniak767 ▴ 740
12
votes
5
replies
5.7k
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 10 months ago by ★ 5.0k • written 9.6 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
6.7k
views
Log2 fold change value in DESeq2
deseq2 rnaseq
written 8.3 years ago by • 0
9
votes
12
replies
12k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
written 9.8 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 7 months ago by 53k • written 12.6 years ago by ▴ 140
34 results • Page 1 of 1
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Answer: Issue loading and downloading Bioconductor 3.22 packages after update by Robert Castelo ★ 3.4k
Hi, the package you refer to is not called `SNPlocs.HSapiens.dbSNP155.GRCh38`, but `SNPlocs.Hsapiens.dbSNP155.GRCh38`, note the lowercase l…
Comment: Issue loading and downloading Bioconductor 3.22 packages after update by ATpoint ★ 5.0k
"Breaks" needs a more detailed explanation, together with code and error messages. Can you confirm it's not just the R download timeout aft…
Comment: Reproducibility of code in various Bioconductor versions by strawberry3 • 0
Thank you for advice! I have updated Bioconductor to the newest one, but now some of my commands don't work anymore, and I cannot download …
Answer: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
I'm not familiar with the packages you mention, but the whole reason why Bioconductor has versions is that code and annotation change. Code…
Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Votes
Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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