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
7 days ago lianov • 0
3
votes
6
replies
997
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
498
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
246
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
685
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
975
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
5 months ago mohammedtoufiq91 ▴ 10
0
votes
5
replies
964
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
624
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
346
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
536
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
460
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
999
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
705
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
4
votes
2
replies
1.1k
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 13 months ago by ★ 5.0k • written 13 months ago by ▴ 10
1
vote
5
replies
1.1k
views
Deseq2 Design
RNASeq DESeq2
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
2
replies
987
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 13 months ago by 53k • written 13 months ago by ▴ 10
0
votes
1
reply
774
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 14 months ago by • 0
0
votes
1
reply
462
views
eRNAs count
RNASeq DESeq2
updated 14 months ago by ★ 5.0k • 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
0
votes
0
replies
419
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
14 months ago brayas13 • 0
2
votes
4
replies
989
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
15 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
1.2k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 15 months ago by 68k • written 15 months ago by • 0
1
vote
2
replies
946
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 15 months ago by 43k • written 15 months ago by ▴ 10
0
votes
3
replies
1.3k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
15 months ago Travis • 0
0
votes
5
replies
2.4k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.7 years ago by • 0
0
votes
2
replies
1.7k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
3
votes
5
replies
2.5k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
2
votes
3
replies
1.4k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
17 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 18 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
2.8k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
18 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 18 months ago by • 0
0
votes
0
replies
762
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
18 months ago JG13 • 0
1,411 results • Page 1 of 29
Recent ...
Replies
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 …
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 20
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Votes
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)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
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