Showing : RNASeq • reset
3
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6
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710
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 25 days ago by • 0
0
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2
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443
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 15 days ago by • 0 • written 12 weeks ago by • 0
0
votes
1
reply
219
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 10 weeks ago by 53k • written 10 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 11 weeks ago by 53k • written 3 months ago by • 0
0
votes
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
993
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
653
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
replies
911
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
4 months ago mohammedtoufiq91 ▴ 10
0
votes
5
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905
views
WGCNA
WGCNA Normalization RNASeq
written 9 months ago by • 0
3
votes
2
replies
1.4k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 6 months ago by ▴ 20
0
votes
1
reply
589
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
1.3k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 6 months ago by ▴ 110 • written 6 months ago by ▴ 10
0
votes
0
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325
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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
3.3k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
7 months ago • updated 9 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
1.2k
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
478
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 9 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
417
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
883
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
664
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
918
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
929
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
940
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
718
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 12 months ago by ★ 5.0k • written 12 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
437
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
407
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
927
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
907
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 14 months ago by 43k • written 14 months ago by ▴ 10
0
votes
3
replies
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
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 16 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
replies
725
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
17 months ago JG13 • 0
0
votes
1
reply
737
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 18 months ago by 68k • written 18 months ago by • 0
1
vote
9
replies
3.3k
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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Replies
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 …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
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…
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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