Showing : Rnaseq • reset
0
votes
1
reply
86
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 days ago by 53k • written 9 days ago by • 0
0
votes
0
replies
88
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 20 hours ago by 43k • written 23 days ago by • 0
5
votes
13
replies
996
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 17 days ago by 53k • written 29 days ago by • 0
0
votes
1
reply
3.0k
views
Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 10.9 years ago by • 0
2
votes
9
replies
761
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
8 weeks ago mohammedtoufiq91 ▴ 10
0
votes
8
replies
541
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
9 weeks ago Jiahao Tian • 0
3
votes
11
replies
1.9k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 12 months ago by • 0
3
votes
2
replies
804
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
11 weeks ago mohammedtoufiq91 ▴ 10
0
votes
5
replies
715
views
WGCNA
WGCNA Normalization RNASeq
written 7 months ago by • 0
3
votes
2
replies
1.3k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 4 months ago by ▴ 20
0
votes
1
reply
486
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 4 months ago by 43k • written 5 months ago by • 0
2
votes
5
replies
1.3k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 4 months ago by ▴ 110 • written 4 months ago by ▴ 10
0
votes
0
replies
247
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
4 months ago dudwnsrla1 • 0
3
votes
7
replies
3.0k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
5 months ago • updated 3 days ago massimo • 0
1
vote
1
reply
1.2k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
votes
4
replies
1.1k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 6 months ago by • 0
0
votes
0
replies
423
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
6 months ago GT • 0
0
votes
3
replies
883
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 7 months ago by 43k • written 7 months ago by • 0
1
vote
2
replies
1.3k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
1
reply
360
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
3
replies
802
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 8 months ago by • 0 • written 8 months ago by ▴ 10
0
votes
1
reply
482
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
2
replies
819
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
8 months ago • updated 7 months ago ingrid.h • 0
0
votes
4
replies
1.3k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
8 months ago Quang NN ▴ 10
0
votes
3
replies
848
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 9 months ago by • 0
4
votes
2
replies
940
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 9 months ago by ★ 5.0k • written 10 months ago by ▴ 10
1
vote
5
replies
946
views
Deseq2 Design
RNASeq DESeq2
updated 9 months ago by 68k • written 10 months ago by • 0
0
votes
2
replies
845
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 10 months ago by 53k • written 10 months ago by ▴ 10
0
votes
1
reply
595
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
1
vote
5
replies
1.1k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 10 months ago by • 0
0
votes
1
reply
391
views
eRNAs count
RNASeq DESeq2
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
1
vote
8
replies
2.4k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 11 months ago by • 0
0
votes
0
replies
364
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
11 months ago brayas13 • 0
2
votes
4
replies
834
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
12 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
943
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 12 months ago by 68k • written 12 months ago by • 0
1
vote
2
replies
828
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 12 months ago by 43k • written 12 months ago by ▴ 10
0
votes
3
replies
1.0k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
12 months ago Travis • 0
0
votes
5
replies
2.2k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.4 years ago by • 0
0
votes
2
replies
1.5k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 13 months ago by ★ 1.4k • written 13 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 14 months ago by ★ 1.4k • written 14 months ago by • 0
2
votes
3
replies
1.2k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
14 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 14 months ago by • 0
4
votes
3
replies
1.5k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 14 months ago by ▴ 10
0
votes
3
replies
941
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
4
replies
2.4k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
15 months ago • updated 14 months ago Lucy ▴ 60
0
votes
4
replies
1.0k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 15 months ago by • 0
0
votes
0
replies
661
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
15 months ago JG13 • 0
0
votes
1
reply
653
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 15 months ago by 68k • written 15 months ago by • 0
1
vote
9
replies
3.1k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 16 months ago by 68k • written 16 months ago by ▴ 10
1
vote
3
replies
941
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 16 months ago by 68k • written 16 months ago by ▴ 50
1,409 results • Page 1 of 29
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Awards • All
Popular Question to Michael Love 43k
Popular Question to Peter • 0
Popular Question to Travis • 0
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Locations • All
The city by the bay, 28 minutes ago
Gurugram, India, 1 hour ago
WEHI, Melbourne, Australia, 2 hours ago
United States, 4 hours ago
United States, 4 hours ago
Traffic: 855 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