Showing : RNASeq • reset
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2
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230
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Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
updated 10 hours ago by 52k • written 1 day ago by • 0
1
vote
1
reply
998
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 18 days ago by ★ 4.8k • written 18 days ago by • 0
0
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4
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638
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 6 weeks ago by • 0
0
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0
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182
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
6 weeks ago GT • 0
0
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2
replies
414
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WGCNA
WGCNA Normalization RNASeq
updated 9 weeks ago by • 0 • written 9 weeks ago by • 0
0
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3
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622
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
1
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2
replies
1.1k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 10 weeks ago by ★ 4.8k • written 10 weeks ago by • 0
0
votes
1
reply
198
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 10 weeks ago by 43k • written 11 weeks ago by • 0
0
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3
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512
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 12 weeks ago by • 0 • written 3 months ago by ▴ 10
0
votes
1
reply
286
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 12 weeks ago by 43k • written 3 months ago by • 0
0
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2
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613
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
3 months ago • updated 10 weeks ago ingrid.h • 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
3 months ago Quang NN ▴ 10
0
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3
replies
661
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 3 months ago by • 0
4
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2
replies
659
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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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739
views
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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621
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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
reply
384
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
1
vote
5
replies
787
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 5 months ago by • 0
0
votes
1
reply
256
views
eRNAs count
RNASeq DESeq2
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
1
vote
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
0
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0
replies
249
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
5 months ago brayas13 • 0
3
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11
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1.1k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 6 months ago by • 0
2
votes
4
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619
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
6 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
668
views
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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656
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 7 months ago by 43k • written 7 months ago by ▴ 10
0
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3
replies
765
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
7 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 4.0 years ago by • 0
0
votes
2
replies
1.2k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
3
votes
5
replies
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
2
votes
3
replies
916
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
8 months ago BioinfGuru ▴ 70
3
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6
replies
1.0k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 9 months ago by • 0
4
votes
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
0
votes
3
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758
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
vote
4
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2.0k
views
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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4
replies
809
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 9 months ago by • 0
0
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0
replies
523
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
10 months ago JG13 • 0
0
votes
1
reply
499
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 10 months ago by 68k • written 10 months ago by • 0
1
vote
9
replies
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
vote
3
replies
776
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
votes
2
replies
805
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 atan • 0
3
votes
2
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903
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
11 months ago mohammedtoufiq91 ▴ 10
0
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0
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435
views
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
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
1
vote
3
replies
842
views
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
votes
3
replies
1.1k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 12 months ago by ★ 4.8k • written 12 months ago by • 0
0
votes
1
reply
688
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
2
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583
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 12 months ago by • 0
0
votes
2
replies
908
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
12 months ago catv • 0
5
votes
3
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1.3k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 11 months ago by 52k • written 12 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Module membership vs gene significance result and Modules-trait relationships re by Vinaya • 0
Hi. I am having the same issue, and haven't found a solution still.
Comment: Feature Counts - potential bug with outfile.jcounts by Tom • 0
[Penistone Locksmith][1] I think that would be a great idea; a novel junction to annotated junction proximity output column. So if the nove…
Comment: Filtering after DESeq by caroline.zanchi • 0
I am going to try this right now, thanks !
Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Votes
Answer: CluserProfiler message "No gene can be mapped"
A: Minfi issue: return code from pthread_create() is 22
Comment: Filtering after DESeq
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
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