Showing : RNASEQ • reset
0
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5
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225
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Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 7 days ago by 43k • written 7 days ago by • 0
3
votes
4
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304
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Question about the filterByExpr function inputs in edgeR
RNASeq filter design edgeR model.matrix
20 days ago • updated 19 days ago mohammedtoufiq91 ▴ 10
8
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8
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2.9k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
written 7.4 years ago by ▴ 20
0
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0
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106
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Job: Job:Computational Biologist position at the University of Alabama at Birmingham
hiring RNASeq JobPosting SingleCell SpatialData
29 days ago lianov • 0
3
votes
6
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1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 10 weeks ago by • 0
0
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2
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551
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 9 weeks ago by • 0 • written 4 months ago by • 0
0
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1
reply
264
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 3 months ago by 53k • written 4 months ago by • 0
5
votes
13
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1.6k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 months ago by 53k • written 4 months ago by • 0
0
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1
reply
3.3k
views
Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 11.3 years ago by • 0
2
votes
9
replies
1.1k
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
5 months ago mohammedtoufiq91 ▴ 10
0
votes
8
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715
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago • updated 5 months ago Jiahao Tian • 0
3
votes
13
replies
2.4k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
3
votes
2
replies
1.1k
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
6 months ago mohammedtoufiq91 ▴ 10
0
votes
5
replies
1.0k
views
WGCNA
WGCNA Normalization RNASeq
written 11 months ago by • 0
3
votes
2
replies
1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
0
votes
1
reply
650
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 8 months ago by 43k • written 8 months ago by • 0
2
votes
5
replies
1.8k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 8 months ago by ▴ 110 • written 8 months ago by ▴ 10
0
votes
0
replies
371
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
8 months ago dudwnsrla1 • 0
4
votes
7
replies
3.5k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
9 months ago • updated 3 months ago massimo ▴ 10
1
vote
1
reply
1.4k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
votes
4
replies
1.5k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 10 months ago by • 0
0
votes
0
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640
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
10 months ago GT • 0
0
votes
3
replies
1.2k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
1
vote
2
replies
1.4k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
votes
1
reply
484
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 11 months ago by 43k • written 12 months ago by • 0
0
votes
3
replies
1.1k
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 12 months ago by • 0 • written 12 months ago by ▴ 10
0
votes
1
reply
750
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
0
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2
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1.0k
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
12 months ago • updated 11 months ago ingrid.h • 0
0
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4
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1.5k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
12 months ago Quang NN ▴ 10
0
votes
3
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1.1k
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 13 months ago by • 0
4
votes
2
replies
1.3k
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 13 months ago by ★ 5.0k • written 13 months ago by ▴ 10
1
vote
5
replies
1.2k
views
Deseq2 Design
RNASeq DESeq2
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
2
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1.0k
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 14 months ago by 53k • written 14 months ago by ▴ 10
0
votes
1
reply
805
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
5
replies
1.4k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 14 months ago by • 0
0
votes
1
reply
476
views
eRNAs count
RNASeq DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
8
replies
2.8k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 15 months ago by • 0
0
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0
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428
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
15 months ago brayas13 • 0
2
votes
4
replies
1.1k
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
16 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
1.3k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 16 months ago by 68k • written 16 months ago by • 0
1
vote
2
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969
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 16 months ago by 43k • written 16 months ago by ▴ 10
0
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3
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1.4k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
16 months ago Travis • 0
0
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5
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2.4k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.7 years ago by • 0
0
votes
2
replies
1.8k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
3
votes
5
replies
2.7k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 17 months ago by ★ 1.4k • written 18 months ago by • 0
2
votes
3
replies
1.4k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
18 months ago • updated 17 months ago BioinfGuru ▴ 70
3
votes
6
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1.4k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 18 months ago by • 0
4
votes
3
replies
1.7k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 18 months ago by ▴ 10
0
votes
3
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1.1k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
1
vote
4
replies
3.0k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
19 months ago • updated 18 months ago Lucy ▴ 60
1,413 results • Page 1 of 29
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Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
Answer: Confused about the CPM and TMM normalization in edgeR
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