Showing : RnaSeq • reset
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979
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 12 days ago by ★ 4.8k • written 13 days ago by • 0
2
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4
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1.7k
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deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 4 weeks ago by 43k • written 2.8 years ago by ▴ 10
0
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4
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598
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 5 weeks ago by • 0
0
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0
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170
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
5 weeks ago GT • 0
1
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8
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1.9k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 5 months ago by • 0
3
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5
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5.0k
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plotMDS in edgeR
edger rnaseq
written 9.6 years ago by ▴ 30
1
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3
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4.9k
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Log2 fold change value in DESeq2
deseq2 rnaseq
written 7.5 years ago by • 0
0
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3
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613
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
0
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2
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398
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WGCNA
WGCNA Normalization RNASeq
updated 8 weeks ago by • 0 • written 8 weeks ago by • 0
1
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2
replies
1.1k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 9 weeks ago by ★ 4.8k • written 9 weeks ago by • 0
0
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2
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593
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
12 weeks ago • updated 9 weeks ago ingrid.h • 0
1
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6
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7.0k
views
GSVA on RNAseq data
gsva rnaseq
updated 10 weeks ago by ★ 3.4k • written 6.0 years ago by ▴ 60
0
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1
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187
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
0
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3
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647
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 3 months ago by • 0
0
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3
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492
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 weeks ago by • 0 • written 12 weeks ago by ▴ 10
1
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5
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780
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 5 months ago by • 0
0
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1
reply
278
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
0
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4
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1.0k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
12 weeks ago Quang NN ▴ 10
4
votes
2
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639
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 4 months ago by ★ 4.8k • written 4 months ago by ▴ 10
1
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5
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730
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Deseq2 Design
RNASeq DESeq2
updated 4 months ago by 68k • written 4 months ago by • 0
0
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2
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613
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 4 months ago by 52k • written 4 months ago by ▴ 10
0
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1
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372
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
0
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1
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250
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eRNAs count
RNASeq DESeq2
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
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0
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241
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
5 months ago brayas13 • 0
11
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3
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2.6k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
written 17 months ago by • 0
3
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11
replies
1.1k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 6 months ago by • 0
2
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4
replies
615
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
6 months ago jihoon.kim.1495 ▴ 10
1
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1
reply
640
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 6 months ago by 68k • written 6 months ago by • 0
1
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2
replies
648
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 months ago by 43k • written 7 months ago by ▴ 10
0
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3
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742
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
6 months ago Travis • 0
0
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5
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2.0k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.9 years ago by • 0
0
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2
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1.2k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
0
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9
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16k
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How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2 pvalue visualization enhancedvolcano rnaseq
written 6.2 years ago by • 0
2
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3
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896
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
8 months ago BioinfGuru ▴ 70
3
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5
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1.8k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
5
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8
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24k
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Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 8 months ago by ▴ 60 • written 2.8 years ago by ▴ 30
0
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4
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801
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 9 months ago by • 0
4
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3
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1.4k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 9 months ago by ▴ 10
3
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6
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1.0k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 9 months ago by • 0
0
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3
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744
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 9 months ago by ★ 4.8k • written 9 months ago by • 0
1
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4
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2.0k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
9 months ago Lucy ▴ 60
0
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3
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1.9k
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 9 months ago by • 0 • written 2.4 years ago by • 0
0
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0
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516
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
10 months ago JG13 • 0
0
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1
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495
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 10 months ago by 68k • written 10 months ago by • 0
1
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9
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2.5k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 10 months ago by 68k • written 10 months ago by ▴ 10
1
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3
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767
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 10 months ago by 68k • written 10 months ago by ▴ 50
2
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2
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796
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 10 months ago by ▴ 10 • written 11 months ago by • 0
0
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6
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1.8k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
11 months ago • updated 10 months ago atan • 0
0
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4
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1.2k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 2.4 years ago by • 0
10
votes
11
replies
2.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 11 months ago by • 0 • written 7.7 years ago by ▴ 80
50 results • Page 1 of 1
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Comment: RNA Seq using Lrt by Rob • 0
So if I have understood what you have said : If i want to see if Day (time) has an effect / is being tested - then the reduced model should…
Comment: How to convert transcript counts to gene counts in R? by ben • 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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