Showing : RNAseq • reset
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 3 days ago by ★ 4.8k • written 4 days ago by • 0
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4
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525
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 27 days ago by • 0
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0
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146
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
29 days ago GT • 0
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2
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384
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WGCNA
WGCNA Normalization RNASeq
updated 7 weeks ago by • 0 • written 7 weeks ago by • 0
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3
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598
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
1
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2
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1.1k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 8 weeks ago by ★ 4.8k • written 8 weeks ago by • 0
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1
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181
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
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3
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461
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 10 weeks ago by • 0 • written 11 weeks ago by ▴ 10
0
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1
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263
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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2
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575
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
10 weeks ago • updated 8 weeks ago ingrid.h • 0
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4
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1.0k
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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
11 weeks ago • updated 10 weeks ago Quang NN ▴ 10
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3
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621
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 3 months ago by • 0
4
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2
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602
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 3 months ago by ★ 4.8k • written 4 months ago by ▴ 10
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5
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710
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Deseq2 Design
RNASeq DESeq2
updated 3 months ago by 68k • written 4 months ago by • 0
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2
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599
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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
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352
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 4 months ago by ★ 4.8k • written 4 months ago by • 0
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5
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753
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 4 months ago by • 0
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1
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240
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eRNAs count
RNASeq DESeq2
updated 4 months ago by ★ 4.8k • written 4 months ago by • 0
1
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8
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1.8k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 5 months ago by • 0
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230
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
5 months ago brayas13 • 0
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1.1k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 6 months ago by • 0
2
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4
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597
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
6 months ago jihoon.kim.1495 ▴ 10
1
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600
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 6 months ago by 68k • written 6 months ago by • 0
1
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2
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637
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 months ago by 43k • written 6 months ago by ▴ 10
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3
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714
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
6 months ago Travis • 0
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5
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2.0k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.9 years ago by • 0
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2
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1.2k
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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
3
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5
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1.7k
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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
2
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3
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864
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
8 months ago BioinfGuru ▴ 70
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6
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1.0k
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 8 months ago by • 0
4
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3
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1.4k
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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 9 months ago by ▴ 10
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3
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730
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 8 months ago by ★ 4.8k • written 8 months ago by • 0
1
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4
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1.9k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
9 months ago • updated 8 months ago Lucy ▴ 60
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4
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785
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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
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0
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502
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
9 months ago JG13 • 0
0
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1
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490
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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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2.4k
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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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758
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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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788
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 10 months ago by ▴ 10 • written 10 months ago by • 0
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6
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1.8k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
10 months ago atan • 0
3
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2
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872
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
10 months ago mohammedtoufiq91 ▴ 10
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413
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
11 months ago Bibi • 0
10
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11
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2.6k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 10 months ago by • 0 • written 7.6 years ago by ▴ 80
1
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3
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826
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 11 months ago by 52k • written 11 months ago by • 0
0
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3
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1.1k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
0
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1
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672
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
0
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2
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570
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 11 months ago by • 0
0
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2
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856
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
12 months ago • updated 11 months ago catv • 0
5
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3
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1.2k
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Log-cpm values from limma
limma edgeR RNASeq
updated 11 months ago by 52k • written 12 months ago by • 0
0
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1
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951
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 12 months ago by 43k • written 12 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: error in ChAMP loading file by barkerxavierr • 0
You have saved your pd object as 'SampleSheet', which is not what champ.load is reading in (it's finding the semi-colon separated file call…
Answer: DiffBind - question on the use of filtered or unfiltered input data by apkffh4x • 0
Yes, you can use HR peaks as input to DiffBind, especially if your goal is high-confidence differential binding, but using all peaks provid…
Answer: Log2foldchange strange behavior by ATpoint ★ 4.8k
The `results()` output you show is perfectly in line with the oputput of `plotCounts()`, hence it is not a DESeq2 issue. UBE3A is higher in…
Comment: DeSeq Strategies for run to run Replication by i.c.denhond • 0
Dear Michael, could you please comment on how to properly apply a vst transformation to a new dataset (in this case, left-out samples)? I …
Comment: Log2foldchange strange behavior by RambakKulit • 0
Okay, I'm attaching those now. Just to provide a bit more context for the results below: I downloaded both count and TPM data from the GTEx…
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