Showing : RNASeq • reset
3
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6
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520
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 15 days ago by • 0
0
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2
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405
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 5 days ago by • 0 • written 11 weeks ago by • 0
0
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1
reply
203
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 8 weeks ago by 53k • written 9 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 10 weeks ago by 53k • written 12 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 11.1 years ago by • 0
2
votes
9
replies
955
views
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
votes
8
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627
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
4 months ago • updated 3 months ago Jiahao Tian • 0
3
votes
13
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2.2k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 14 months ago by • 0
3
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2
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887
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
4 months ago mohammedtoufiq91 ▴ 10
0
votes
5
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888
views
WGCNA
WGCNA Normalization RNASeq
written 9 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 6 months ago by ▴ 20
0
votes
1
reply
573
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 6 months ago by 43k • written 6 months ago by • 0
2
votes
5
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1.3k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 6 months ago by ▴ 110 • written 6 months ago by ▴ 10
0
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0
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311
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Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
6 months ago dudwnsrla1 • 0
4
votes
7
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3.3k
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Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
7 months ago • updated 8 weeks ago massimo ▴ 10
1
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1
reply
1.3k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
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
votes
0
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465
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
8 months ago GT • 0
0
votes
3
replies
1000
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 months ago by 43k • written 9 months ago by • 0
1
vote
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
votes
1
reply
407
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 9 months ago by 43k • written 10 months ago by • 0
0
votes
3
replies
866
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 10 months ago by • 0 • written 10 months ago by ▴ 10
0
votes
1
reply
646
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
2
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904
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
10 months ago • updated 9 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
10 months ago Quang NN ▴ 10
0
votes
3
replies
912
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 11 months ago by • 0
4
votes
2
replies
999
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
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5
replies
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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925
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 12 months ago by 53k • written 12 months ago by ▴ 10
0
votes
1
reply
703
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
1
vote
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
423
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 13 months ago by • 0
0
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0
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397
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
13 months ago brayas13 • 0
2
votes
4
replies
908
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
14 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
1.0k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 14 months ago by 68k • written 14 months ago by • 0
1
vote
2
replies
894
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 14 months ago by 43k • written 14 months ago by ▴ 10
0
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3
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1.1k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
14 months ago Travis • 0
0
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5
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2.3k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.6 years ago by • 0
0
votes
2
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1.6k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
3
votes
5
replies
2.3k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
2
votes
3
replies
1.3k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
16 months ago • updated 15 months ago BioinfGuru ▴ 70
3
votes
6
replies
1.4k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 16 months ago by • 0
4
votes
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
votes
3
replies
996
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
1
vote
4
replies
2.6k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
17 months ago • updated 16 months ago Lucy ▴ 60
0
votes
4
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1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 17 months ago by • 0
0
votes
0
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715
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
17 months ago JG13 • 0
0
votes
1
reply
725
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 17 months ago by 68k • written 17 months ago by • 0
1
vote
9
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3.3k
views
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 18 months ago by ▴ 10
1,410 results • Page 1 of 29
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Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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