Showing : RnaSeq • reset
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4
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335
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Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
14 days ago • updated 13 days ago Mariami • 0
0
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5
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298
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Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 27 days ago by 43k • written 27 days ago by • 0
3
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4
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449
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Question about the filterByExpr function inputs in edgeR
RNASeq filter design edgeR model.matrix
5 weeks ago mohammedtoufiq91 ▴ 10
0
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0
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147
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Job: Job:Computational Biologist position at the University of Alabama at Birmingham
hiring RNASeq JobPosting SingleCell SpatialData
7 weeks ago lianov • 0
3
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6
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1.1k
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 3 months ago by • 0
0
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1
reply
290
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
0
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2
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623
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After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 12 weeks ago by • 0 • written 5 months ago by • 0
5
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13
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1.7k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 5 months ago by 53k • written 5 months ago by • 0
2
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9
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1.2k
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
6 months ago mohammedtoufiq91 ▴ 10
0
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8
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756
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago Jiahao Tian • 0
3
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2
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1.2k
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
7 months ago mohammedtoufiq91 ▴ 10
3
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2
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1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
2
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5
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2.0k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 9 months ago by ▴ 110 • written 9 months ago by ▴ 10
0
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0
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404
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Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
9 months ago dudwnsrla1 • 0
0
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1
reply
686
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 9 months ago by 43k • written 9 months ago by • 0
4
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7
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3.6k
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Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
10 months ago • updated 4 months ago massimo ▴ 10
1
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1
reply
1.5k
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
votes
4
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1.6k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 11 months ago by • 0
0
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0
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781
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
11 months ago GT • 0
0
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5
replies
1.1k
views
WGCNA
WGCNA Normalization RNASeq
written 12 months ago by • 0
0
votes
3
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1.2k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 12 months ago by 43k • written 12 months ago by • 0
1
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2
replies
1.5k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
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1
reply
513
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 12 months ago by 43k • written 12 months ago by • 0
0
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1
reply
786
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
0
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2
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1.1k
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
13 months ago • updated 12 months ago ingrid.h • 0
0
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3
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1.2k
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 12 months ago by • 0 • written 13 months ago by ▴ 10
0
votes
4
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1.5k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
13 months ago Quang NN ▴ 10
0
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3
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1.1k
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 13 months ago by • 0
1
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5
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1.2k
views
Deseq2 Design
RNASeq DESeq2
updated 14 months ago by 68k • written 14 months ago by • 0
4
votes
2
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1.4k
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 14 months ago by ★ 5.0k • written 14 months ago by ▴ 10
0
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2
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1.1k
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 14 months ago by 53k • written 14 months ago by ▴ 10
0
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1
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841
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
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5
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1.5k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 15 months ago by • 0
0
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1
reply
485
views
eRNAs count
RNASeq DESeq2
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
0
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0
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436
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
15 months ago brayas13 • 0
1
vote
8
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3.0k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 15 months ago by • 0
2
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4
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1.1k
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
16 months ago jihoon.kim.1495 ▴ 10
3
votes
13
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2.4k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
1
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1
reply
1.4k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 17 months ago by 68k • written 17 months ago by • 0
0
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3
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1.6k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
17 months ago Travis • 0
1
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2
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1.0k
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 17 months ago by 43k • written 17 months ago by ▴ 10
0
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2
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2.0k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
2
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3
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1.4k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
18 months ago BioinfGuru ▴ 70
3
votes
5
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2.8k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
3
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6
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1.5k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 19 months ago by • 0
0
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3
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1.1k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
4
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3
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1.7k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 19 months ago by ▴ 10
0
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4
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1.2k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 19 months ago by • 0
1
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4
replies
3.1k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
19 months ago Lucy ▴ 60
0
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0
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828
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
20 months ago JG13 • 0
1,414 results • Page 1 of 29
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Answer: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
I'm not familiar with the packages you mention, but the whole reason why Bioconductor has versions is that code and annotation change. Code…
Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Votes
Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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