Showing : RnaSeq • reset
1
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2
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56
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Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
updated 6 hours ago by 53k • written 11 hours ago by • 0
0
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5
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251
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 13 days ago by 43k • written 13 days ago by • 0
3
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4
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362
views
Question about the filterByExpr function inputs in edgeR
RNASeq filter design edgeR model.matrix
27 days ago • updated 26 days ago mohammedtoufiq91 ▴ 10
8
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8
replies
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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123
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Job: Job:Computational Biologist position at the University of Alabama at Birmingham
hiring RNASeq JobPosting SingleCell SpatialData
5 weeks ago lianov • 0
3
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6
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1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 11 weeks ago by • 0
0
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2
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570
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After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 10 weeks ago by • 0 • written 4 months ago by • 0
3
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13
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2.4k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
9
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12
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11k
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Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
written 9.7 years ago by ▴ 20
0
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3
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1.5k
views
PCA subset of genes vs DE
DESeq2 RNASeq
written 3.0 years ago by ▴ 20
0
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2
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1.4k
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq splicing RNAseq DEXSeq
written 6.2 years ago by ▴ 10
4
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7
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3.6k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
9 months ago • updated 4 months ago massimo ▴ 10
0
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1
reply
273
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
5
votes
13
replies
1.6k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 months ago by 53k • written 5 months ago by • 0
0
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1
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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
3
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7
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2.1k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
24 months ago • updated 5 months ago boczniak767 ▴ 740
2
votes
9
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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
6 months ago mohammedtoufiq91 ▴ 10
0
votes
8
replies
729
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago Jiahao Tian • 0
3
votes
5
replies
2.0k
views
weird model design for DE analysis
RNASeq
updated 6 months ago by 53k • written 12.6 years ago by ▴ 140
3
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2
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1.1k
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
6 months ago mohammedtoufiq91 ▴ 10
0
votes
5
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1.1k
views
WGCNA
WGCNA Normalization RNASeq
written 11 months ago by • 0
3
votes
2
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1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
12
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5
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5.5k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 8 months ago by • 0 • written 2.2 years ago by • 0
0
votes
1
reply
663
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 8 months ago by 43k • written 9 months ago by • 0
2
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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
384
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Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
8 months ago dudwnsrla1 • 0
8
votes
10
replies
18k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 9 months ago by ★ 5.0k • written 9.5 years ago by ▴ 20
1
vote
1
reply
1.4k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
2
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4
replies
2.5k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 10 months ago by 43k • written 3.6 years ago by ▴ 10
0
votes
4
replies
1.6k
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
replies
681
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
11 months ago GT • 0
1
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8
replies
2.9k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 15 months ago by • 0
3
votes
5
replies
5.4k
views
plotMDS in edgeR
edger rnaseq
written 10.4 years ago by ▴ 30
1
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3
replies
6.6k
views
Log2 fold change value in DESeq2
deseq2 rnaseq
written 8.3 years ago by • 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
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2
replies
1.5k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
votes
2
replies
1.1k
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
12 months ago ingrid.h • 0
1
vote
6
replies
8.0k
views
GSVA on RNAseq data
gsva rnaseq
updated 12 months ago by ★ 3.4k • written 6.8 years ago by ▴ 60
0
votes
1
reply
502
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 12 months ago by 43k • written 12 months ago by • 0
39 results • Page 1 of 1
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Answer: Bulk RNAseq analysis for by Gordon Smyth 53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Comment: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open fo by a2a2haa • 0
By promoting reproducible analysis, the scientific community can better understand the precise mechanisms that make [Hydrogen inhalation sa…
Answer: Bulk RNAseq analysis for by James W. MacDonald 68k
In my experience, the within-clone variability of differentiated stem cells is often as large or larger than the between-clone variability,…
Comment: Jobs at Ensembl by frostybuddyy • 0
I found your blog "Jobs at Ensembl" quite fascinating! The way you talked about the convergence of bioinformatics and data science in emplo…
Comment: Postdoctoral Fellow (Computational Biology / Bioinformatics) - Neuroepigenetics by mudasarnaeem2020 • 0
Promoting UDISE+ Features on Social Media to Increase Awareness https://udisseplus.com/[enter link description here][1] [1]: https://ud…
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Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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