Showing : rnaseq • reset
0
votes
1
reply
247
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 3 days ago by ★ 4.0k • written 7 weeks ago by • 0
0
votes
1
reply
175
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 5 weeks ago by 53k • written 5 weeks ago by • 0
5
votes
13
replies
1.2k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 6 weeks ago by 53k • written 8 weeks 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 11.0 years ago by • 0
2
votes
9
replies
921
views
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
votes
8
replies
594
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
3 months ago Jiahao Tian • 0
3
votes
13
replies
2.1k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 13 months ago by • 0
3
votes
2
replies
855
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
3 months ago mohammedtoufiq91 ▴ 10
0
votes
5
replies
841
views
WGCNA
WGCNA Normalization RNASeq
written 8 months ago by • 0
3
votes
2
replies
1.4k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 5 months ago by ▴ 20
0
votes
1
reply
548
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 5 months ago by 43k • written 6 months ago by • 0
2
votes
5
replies
1.3k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 5 months ago by ▴ 110 • written 5 months ago by ▴ 10
0
votes
0
replies
298
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
5 months ago dudwnsrla1 • 0
4
votes
7
replies
3.3k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
6 months ago • updated 5 weeks ago massimo ▴ 10
1
vote
1
reply
1.3k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 7 months ago by ★ 5.0k • written 7 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 7 months ago by • 0
0
votes
0
replies
449
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
7 months ago GT • 0
0
votes
3
replies
961
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
1
vote
2
replies
1.3k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 8 months ago by ★ 5.0k • written 9 months ago by • 0
0
votes
1
reply
387
views
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
votes
3
replies
843
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 9 months ago by • 0 • written 9 months ago by ▴ 10
0
votes
1
reply
595
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
2
replies
878
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
9 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
9 months ago Quang NN ▴ 10
0
votes
3
replies
888
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 10 months ago by • 0
4
votes
2
replies
967
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 10 months ago by ★ 5.0k • written 11 months ago by ▴ 10
1
vote
5
replies
1.0k
views
Deseq2 Design
RNASeq DESeq2
updated 10 months ago by 68k • written 11 months ago by • 0
0
votes
2
replies
882
views
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
votes
1
reply
665
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
1
vote
5
replies
1.2k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 11 months ago by • 0
0
votes
1
reply
406
views
eRNAs count
RNASeq DESeq2
updated 11 months ago by ★ 5.0k • written 11 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 12 months ago by • 0
0
votes
0
replies
386
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
12 months ago brayas13 • 0
2
votes
4
replies
875
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
13 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
997
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 13 months ago by 68k • written 13 months ago by • 0
1
vote
2
replies
867
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 13 months ago by 43k • written 13 months ago by ▴ 10
0
votes
3
replies
1.1k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
13 months ago Travis • 0
0
votes
5
replies
2.3k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.5 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 14 months ago by ★ 1.4k • written 14 months ago by • 0
3
votes
5
replies
2.2k
views
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
votes
3
replies
1.3k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
15 months ago BioinfGuru ▴ 70
3
votes
6
replies
1.3k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 15 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 16 months ago by ▴ 10
0
votes
3
replies
974
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
vote
4
replies
2.5k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
16 months ago • updated 15 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 16 months ago by • 0
0
votes
0
replies
696
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
16 months ago JG13 • 0
0
votes
1
reply
694
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 17 months ago by 68k • written 17 months ago by • 0
1
vote
9
replies
3.2k
views
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
vote
3
replies
1.0k
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 17 months ago by 68k • written 17 months ago by ▴ 50
1,409 results • Page 1 of 29
Recent ...
Replies
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Awards • All
Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
Popular Question to Peter Hickey ▴ 760
Popular Question to edward.esiribloom • 0
Locations • All
United States, 41 minutes ago
The city by the bay, 1 hour ago
1201 N Market St Suite 111, Wilmington, DE 19801, United States, 1 hour ago
United States, 3 hours ago
United States, 4 hours ago
Traffic: 1386 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6