Showing : RNAseq • reset
0
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354
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After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 18 hours ago by • 0 • written 9 weeks ago by • 0
3
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5
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179
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
5 days ago • updated 54 minutes ago Ahmed Salah • 0
0
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1
reply
197
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 7 weeks ago by 53k • written 7 weeks ago by • 0
5
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13
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1.2k
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 8 weeks ago by 53k • written 10 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
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9
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943
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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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614
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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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871
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
4 months ago mohammedtoufiq91 ▴ 10
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5
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880
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WGCNA
WGCNA Normalization RNASeq
written 9 months ago by • 0
3
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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
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568
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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
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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 6 months ago by ▴ 110 • written 6 months ago by ▴ 10
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307
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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
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7
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3.3k
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Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
7 months ago • updated 7 weeks ago massimo ▴ 10
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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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457
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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
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3
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987
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
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2
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1.3k
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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
398
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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
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3
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859
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 9 months ago by • 0 • written 10 months ago by ▴ 10
0
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1
reply
637
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
0
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2
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900
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
10 months ago • updated 9 months ago ingrid.h • 0
0
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4
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1.4k
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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
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3
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901
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 10 months ago by • 0
4
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2
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986
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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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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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906
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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
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694
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
1
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5
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1.2k
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 12 months ago by • 0
0
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1
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418
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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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393
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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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898
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
13 months ago jihoon.kim.1495 ▴ 10
1
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1
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1.0k
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 14 months ago by 68k • written 14 months ago by • 0
1
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2
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883
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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
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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
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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
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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
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5
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2.3k
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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
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3
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1.3k
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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
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 16 months ago by • 0
4
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3
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1.6k
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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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987
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
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4
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2.5k
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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
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0
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710
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
17 months ago JG13 • 0
0
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1
reply
714
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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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3.2k
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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
1,410 results • Page 1 of 29
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Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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