Showing : RNAseq • reset
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 1 day ago by 53k • written 6 days ago by • 0
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0
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81
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After running samtools, the featureCounts command crashed.
RNASeqData RNASeq rnaseqGene
21 days ago Rui • 0
5
votes
13
replies
978
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 14 days ago by 53k • written 27 days ago by • 0
0
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1
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3.0k
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Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 10.9 years ago by • 0
2
votes
9
replies
755
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
8 weeks ago mohammedtoufiq91 ▴ 10
0
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8
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535
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
9 weeks ago • updated 8 weeks ago Jiahao Tian • 0
3
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11
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1.9k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 12 months ago by • 0
3
votes
2
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802
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
11 weeks ago • updated 10 weeks ago mohammedtoufiq91 ▴ 10
0
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5
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713
views
WGCNA
WGCNA Normalization RNASeq
written 7 months ago by • 0
3
votes
2
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1.3k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 4 months ago by ▴ 20
0
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1
reply
484
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 4 months ago by 43k • written 4 months ago by • 0
2
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5
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1.3k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 4 months ago by ▴ 110 • written 4 months ago by ▴ 10
0
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0
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244
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Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
4 months ago dudwnsrla1 • 0
3
votes
7
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3.0k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
5 months ago • updated 1 day ago massimo • 0
1
vote
1
reply
1.2k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
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4
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1.1k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 6 months ago by • 0
0
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0
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420
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
6 months ago GT • 0
0
votes
3
replies
877
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 7 months ago by 43k • written 7 months ago by • 0
1
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2
replies
1.3k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
1
reply
359
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 7 months ago by 43k • written 8 months ago by • 0
0
votes
3
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802
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 8 months ago by • 0 • written 8 months ago by ▴ 10
0
votes
1
reply
482
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
0
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2
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818
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
8 months ago • updated 7 months ago ingrid.h • 0
0
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4
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1.3k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
8 months ago Quang NN ▴ 10
0
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3
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847
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 9 months ago by • 0
4
votes
2
replies
940
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 9 months ago by ★ 5.0k • written 10 months ago by ▴ 10
1
vote
5
replies
945
views
Deseq2 Design
RNASeq DESeq2
updated 9 months ago by 68k • written 9 months ago by • 0
0
votes
2
replies
844
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 10 months ago by 53k • written 10 months ago by ▴ 10
0
votes
1
reply
592
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
1
vote
5
replies
1.1k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 10 months ago by • 0
0
votes
1
reply
390
views
eRNAs count
RNASeq DESeq2
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
1
vote
8
replies
2.4k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 11 months ago by • 0
0
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0
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362
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
11 months ago brayas13 • 0
2
votes
4
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828
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
12 months ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
940
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 12 months ago by 68k • written 12 months ago by • 0
1
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2
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827
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 12 months ago by 43k • written 12 months ago by ▴ 10
0
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3
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1.0k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
12 months ago Travis • 0
0
votes
5
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2.2k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.4 years ago by • 0
0
votes
2
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1.5k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
3
votes
5
replies
2.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
2
votes
3
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1.2k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
14 months ago BioinfGuru ▴ 70
3
votes
6
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1.3k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 14 months ago by • 0
4
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3
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1.5k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 14 months ago by ▴ 10
0
votes
3
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937
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
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4
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2.4k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
15 months ago • updated 14 months ago Lucy ▴ 60
0
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4
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1.0k
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 15 months ago by • 0
0
votes
0
replies
661
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
15 months ago JG13 • 0
0
votes
1
reply
650
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 15 months ago by 68k • written 15 months ago by • 0
1
vote
9
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3.1k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 15 months ago by 68k • written 16 months ago by ▴ 10
1
vote
3
replies
939
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 16 months ago by 68k • written 16 months ago by ▴ 50
1,409 results • Page 1 of 29
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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