Showing : rnaseq • reset
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WGCNA
WGCNA Normalization RNASeq
updated 10 days ago by • 0 • written 11 days ago by • 0
0
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3
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497
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 days ago by 43k • written 12 days ago by • 0
1
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2
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1.0k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 16 days ago by ★ 4.7k • written 16 days ago by • 0
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1
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137
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 19 days ago by 43k • written 23 days ago by • 0
0
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3
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376
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 27 days ago by • 0 • written 5 weeks ago by ▴ 10
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1
reply
180
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 4 weeks ago by 43k • written 4 weeks ago by • 0
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2
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521
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
4 weeks ago • updated 16 days ago ingrid.h • 0
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4
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952
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
5 weeks ago • updated 4 weeks ago Quang NN ▴ 10
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3
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534
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 7 weeks ago by • 0
4
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2
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468
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 10 weeks ago by ★ 4.7k • written 11 weeks ago by ▴ 10
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5
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631
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Deseq2 Design
RNASeq DESeq2
updated 10 weeks ago by 68k • written 11 weeks ago by • 0
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2
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537
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 12 weeks ago by 52k • written 12 weeks ago by ▴ 10
0
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1
reply
268
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
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5
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625
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 3 months ago by • 0
0
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1
reply
209
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eRNAs count
RNASeq DESeq2
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
1
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8
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1.4k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 3 months ago by • 0
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0
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191
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
3 months ago brayas13 • 0
3
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11
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926
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 4 months ago by • 0
2
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4
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523
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
4 months ago jihoon.kim.1495 ▴ 10
1
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1
reply
493
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 5 months ago by 68k • written 5 months ago by • 0
1
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2
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575
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 5 months ago by ▴ 10
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3
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604
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
5 months ago Travis • 0
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5
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1.9k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.8 years ago by • 0
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2
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1.1k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
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5
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1.4k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
2
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3
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730
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
6 months ago BioinfGuru ▴ 70
3
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6
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912
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 7 months ago by • 0
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3
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1.3k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 7 months ago by ▴ 10
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3
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668
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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 7 months ago by ★ 4.7k • written 7 months ago by • 0
1
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4
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1.7k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
7 months ago Lucy ▴ 60
0
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4
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709
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 7 months ago by • 0
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440
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
8 months ago JG13 • 0
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450
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 8 months ago by 68k • written 8 months ago by • 0
1
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9
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2.0k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 8 months ago by 68k • written 8 months ago by ▴ 10
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3
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690
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 8 months ago by 68k • written 8 months ago by ▴ 50
2
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2
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731
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 9 months ago by ▴ 10 • written 9 months ago by • 0
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6
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1.6k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
9 months ago atan • 0
3
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2
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797
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
9 months ago mohammedtoufiq91 ▴ 10
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376
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
9 months ago Bibi • 0
10
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11
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2.5k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 9 months ago by • 0 • written 7.5 years ago by ▴ 80
1
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3
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756
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 9 months ago by 52k • written 9 months ago by • 0
0
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3
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976
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 10 months ago by ★ 4.7k • written 10 months ago by • 0
0
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1
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617
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 10 months ago by 43k • written 10 months ago by • 0
0
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527
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 10 months ago by • 0
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2
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744
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
10 months ago catv • 0
5
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3
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1.1k
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Log-cpm values from limma
limma edgeR RNASeq
updated 9 months ago by 52k • written 10 months ago by • 0
0
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1
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794
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 10 months ago by 43k • written 10 months ago by • 0
0
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1
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673
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 10 months ago by ★ 4.7k • written 10 months ago by • 0
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2
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1.4k
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
11 months ago kcarey • 0
2
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2
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601
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
11 months ago Sabiha ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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