Showing : RnaSeq • reset
8
votes
8
replies
2.8k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
written 7.3 years ago by ▴ 20
0
votes
0
replies
59
views
Job: Job:Computational Biologist position at the University of Alabama at Birmingham
hiring RNASeq JobPosting SingleCell SpatialData
8 days ago lianov • 0
3
votes
6
replies
1.0k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 7 weeks ago by • 0
0
votes
2
replies
499
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 6 weeks ago by • 0 • written 3 months ago by • 0
0
votes
1
reply
247
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 3 months ago by 53k • written 3 months ago by • 0
5
votes
13
replies
1.4k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 3 months ago by 53k • written 4 months ago by • 0
0
votes
1
reply
3.2k
views
Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 11.2 years ago by • 0
2
votes
9
replies
1.0k
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
5 months ago mohammedtoufiq91 ▴ 10
0
votes
8
replies
686
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
5 months ago Jiahao Tian • 0
3
votes
13
replies
2.3k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 15 months ago by • 0
3
votes
2
replies
978
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
5 months ago mohammedtoufiq91 ▴ 10
0
votes
5
replies
967
views
WGCNA
WGCNA Normalization RNASeq
written 10 months ago by • 0
3
votes
2
replies
1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 7 months ago by ▴ 20
0
votes
1
reply
625
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 7 months ago by 43k • written 8 months ago by • 0
2
votes
5
replies
1.5k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 7 months ago by ▴ 110 • written 7 months ago by ▴ 10
0
votes
0
replies
347
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
7 months ago dudwnsrla1 • 0
4
votes
7
replies
3.4k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
8 months ago • updated 3 months ago massimo ▴ 10
1
vote
1
reply
1.3k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
votes
4
replies
1.4k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 10 months ago by • 0
0
votes
0
replies
539
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
10 months ago GT • 0
0
votes
3
replies
1.1k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 10 months ago by 43k • written 10 months ago by • 0
1
vote
2
replies
1.4k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
votes
1
reply
462
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
3
replies
1.0k
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 months ago by • 0 • written 11 months ago by ▴ 10
0
votes
1
reply
706
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
2
replies
1.0k
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
11 months ago ingrid.h • 0
0
votes
4
replies
1.4k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
11 months ago Quang NN ▴ 10
0
votes
3
replies
1.0k
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 12 months ago by • 0
1
vote
5
replies
1.3k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 14 months ago by • 0
1
vote
8
replies
2.7k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 14 months ago by • 0
3
votes
7
replies
2.0k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
23 months ago • updated 4 months ago boczniak767 ▴ 740
12
votes
5
replies
5.3k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 7 months ago by • 0 • written 2.1 years ago by • 0
8
votes
10
replies
18k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 8 months ago by ★ 5.0k • written 9.5 years ago by ▴ 20
0
votes
3
replies
1.4k
views
PCA subset of genes vs DE
DESeq2 RNASeq
written 2.9 years ago by ▴ 20
2
votes
4
replies
2.5k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 9 months ago by 43k • written 3.6 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 6.1 years ago by ▴ 10
1
vote
6
replies
7.8k
views
GSVA on RNAseq data
gsva rnaseq
updated 11 months ago by ★ 3.4k • written 6.8 years ago by ▴ 60
1
vote
3
replies
6.1k
views
Log2 fold change value in DESeq2
deseq2 rnaseq
written 8.2 years ago by • 0
9
votes
12
replies
11k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
written 9.6 years ago by ▴ 20
3
votes
5
replies
5.4k
views
plotMDS in edgeR
edger rnaseq
written 10.3 years ago by ▴ 30
3
votes
5
replies
2.0k
views
weird model design for DE analysis
RNASeq
updated 5 months ago by 53k • written 12.5 years ago by ▴ 140
41 results • Page 1 of 1
Recent ...
Replies
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
Awards • All
Commentator to James W. MacDonald 68k
Great Question to fl ▴ 20
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
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