Showing : RNAseq • reset
3
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6
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790
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 29 days ago by • 0
0
votes
2
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456
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 19 days ago by • 0 • written 3 months ago by • 0
0
votes
1
reply
224
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 10 weeks ago by 53k • written 11 weeks ago by • 0
5
votes
13
replies
1.3k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 12 weeks ago by 53k • written 3 months ago by • 0
0
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1
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3.2k
views
Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 11.1 years ago by • 0
2
votes
9
replies
1000
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
4 months ago mohammedtoufiq91 ▴ 10
0
votes
8
replies
654
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
4 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
votes
2
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919
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
4 months ago mohammedtoufiq91 ▴ 10
0
votes
5
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907
views
WGCNA
WGCNA Normalization RNASeq
written 10 months ago by • 0
3
votes
2
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1.4k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 6 months ago by ▴ 20
0
votes
1
reply
598
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 6 months ago by 43k • written 7 months ago by • 0
2
votes
5
replies
1.4k
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
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328
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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
7 months ago • updated 10 weeks ago massimo ▴ 10
1
vote
1
reply
1.3k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
votes
4
replies
1.3k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 9 months ago by • 0
0
votes
0
replies
491
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
9 months ago GT • 0
0
votes
3
replies
1.0k
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 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
votes
1
reply
420
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
3
replies
899
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
670
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
replies
936
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
10 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
934
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 11 months ago by • 0
4
votes
2
replies
1.0k
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 12 months ago by ★ 5.0k • written 12 months ago by ▴ 10
1
vote
5
replies
1.0k
views
Deseq2 Design
RNASeq DESeq2
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
2
replies
947
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
729
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 13 months ago by ★ 5.0k • written 13 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 13 months ago by • 0
0
votes
1
reply
440
views
eRNAs count
RNASeq DESeq2
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
1
vote
8
replies
2.5k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 13 months ago by • 0
0
votes
0
replies
408
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
937
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
14 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
1.1k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 14 months ago by 68k • written 14 months ago by • 0
1
vote
2
replies
912
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 14 months ago by 43k • written 15 months ago by ▴ 10
0
votes
3
replies
1.2k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
15 months ago • updated 14 months ago Travis • 0
0
votes
5
replies
2.3k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.6 years ago by • 0
0
votes
2
replies
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 BioinfGuru ▴ 70
3
votes
6
replies
1.4k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 17 months ago by • 0
4
votes
3
replies
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 17 months ago by ▴ 10
0
votes
3
replies
1.0k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 17 months ago by ★ 5.0k • written 17 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 Lucy ▴ 60
0
votes
4
replies
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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728
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
18 months ago JG13 • 0
0
votes
1
reply
746
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 18 months ago by 68k • written 18 months ago by • 0
1
vote
9
replies
3.4k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 18 months ago by 68k • written 18 months ago by ▴ 10
1,410 results • Page 1 of 29
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Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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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