Showing : RNASEQ • reset
0
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283
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After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
written 8 weeks ago by • 0
0
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1
reply
182
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 5 weeks ago by 53k • written 6 weeks ago by • 0
5
votes
13
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1.2k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 7 weeks ago by 53k • written 9 weeks ago by • 0
0
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1
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3.2k
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Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 11.0 years ago by • 0
2
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9
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930
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Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
3 months ago mohammedtoufiq91 ▴ 10
0
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8
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602
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
3 months ago Jiahao Tian • 0
3
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13
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2.1k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 13 months ago by • 0
3
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2
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864
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
3 months ago mohammedtoufiq91 ▴ 10
0
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5
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857
views
WGCNA
WGCNA Normalization RNASeq
written 8 months ago by • 0
3
votes
2
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1.4k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 5 months ago by ▴ 20
0
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1
reply
552
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 5 months ago by 43k • written 6 months ago by • 0
2
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5
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1.3k
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Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 5 months ago by ▴ 110 • written 5 months ago by ▴ 10
0
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0
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301
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Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
5 months ago dudwnsrla1 • 0
4
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7
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3.3k
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Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
6 months ago • updated 5 weeks ago massimo ▴ 10
1
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1
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1.3k
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
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4
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1.2k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 8 months ago by • 0
0
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0
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453
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
8 months ago GT • 0
0
votes
3
replies
967
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
1
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2
replies
1.3k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
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1
reply
392
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
3
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846
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 9 months ago by • 0 • written 9 months ago by ▴ 10
0
votes
1
reply
614
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
0
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2
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880
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
9 months ago ingrid.h • 0
0
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4
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1.4k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
9 months ago Quang NN ▴ 10
0
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3
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894
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 10 months ago by • 0
4
votes
2
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972
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 11 months ago by ★ 5.0k • written 11 months ago by ▴ 10
1
vote
5
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1.0k
views
Deseq2 Design
RNASeq DESeq2
updated 11 months ago by 68k • written 11 months ago by • 0
0
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2
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888
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 11 months ago by 53k • written 11 months ago by ▴ 10
0
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1
reply
672
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
1
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5
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1.2k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 12 months ago by • 0
0
votes
1
reply
411
views
eRNAs count
RNASeq DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
1
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8
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2.5k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 12 months ago by • 0
0
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0
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389
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
12 months ago brayas13 • 0
2
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4
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879
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
13 months ago jihoon.kim.1495 ▴ 10
1
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1
reply
1.0k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 13 months ago by 68k • written 13 months ago by • 0
1
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2
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873
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 13 months ago by 43k • written 13 months ago by ▴ 10
0
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3
replies
1.1k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
13 months ago Travis • 0
0
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5
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2.3k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.5 years ago by • 0
0
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2
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1.6k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
3
votes
5
replies
2.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
2
votes
3
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1.3k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
15 months ago BioinfGuru ▴ 70
3
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6
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1.3k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 15 months ago by • 0
4
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3
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1.6k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 16 months ago by ▴ 10
0
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3
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974
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
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4
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2.5k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
16 months ago Lucy ▴ 60
0
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4
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1.1k
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 16 months ago by • 0
0
votes
0
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702
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
16 months ago JG13 • 0
0
votes
1
reply
700
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 17 months ago by 68k • written 17 months ago by • 0
1
vote
9
replies
3.2k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 17 months ago by 68k • written 17 months ago by ▴ 10
1
vote
3
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1.0k
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 17 months ago by 68k • written 17 months ago by ▴ 50
1,409 results • Page 1 of 29
Recent ...
Replies
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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