Showing : RnaSeq • reset
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 18 days ago by 53k • written 22 days ago by • 0
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0
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104
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After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 14 days ago by 43k • written 5 weeks ago by • 0
5
votes
13
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1.1k
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 weeks ago by 53k • written 6 weeks 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 11.0 years ago by • 0
2
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9
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844
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Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
10 weeks ago mohammedtoufiq91 ▴ 10
0
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8
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557
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
11 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
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2
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829
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
3 months ago mohammedtoufiq91 ▴ 10
0
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5
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738
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WGCNA
WGCNA Normalization RNASeq
written 8 months ago by • 0
3
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2
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1.3k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 4 months ago by ▴ 20
0
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1
reply
501
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 5 months ago by 43k • written 5 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 5 months ago by ▴ 110 • written 5 months ago by ▴ 10
0
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0
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263
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Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
5 months ago dudwnsrla1 • 0
4
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7
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3.2k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
6 months ago • updated 17 days ago massimo ▴ 10
1
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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
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 7 months ago by • 0
0
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0
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435
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
7 months ago GT • 0
0
votes
3
replies
908
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
1
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2
replies
1.3k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
votes
1
reply
372
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
3
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817
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 8 months ago by • 0 • written 9 months ago by ▴ 10
0
votes
1
reply
495
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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838
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
8 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
9 months ago • updated 8 months ago Quang NN ▴ 10
0
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3
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863
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 9 months ago by • 0
4
votes
2
replies
951
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 10 months ago by ★ 5.0k • written 10 months ago by ▴ 10
1
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5
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972
views
Deseq2 Design
RNASeq DESeq2
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
2
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859
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
608
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
1
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5
replies
1.1k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 11 months ago by • 0
0
votes
1
reply
396
views
eRNAs count
RNASeq DESeq2
updated 11 months ago by ★ 5.0k • written 11 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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373
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
11 months ago brayas13 • 0
2
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4
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844
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
12 months ago jihoon.kim.1495 ▴ 10
1
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1
reply
966
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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847
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 13 months ago by 43k • written 13 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
13 months ago Travis • 0
0
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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 14 months ago by ★ 1.4k • written 14 months ago by • 0
3
votes
5
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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
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3
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1.2k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
14 months ago BioinfGuru ▴ 70
3
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6
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1.3k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 15 months ago by • 0
4
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3
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1.6k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 15 months ago by ▴ 10
0
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3
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956
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
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4
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2.4k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
15 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
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0
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676
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
16 months ago JG13 • 0
0
votes
1
reply
668
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 16 months ago by 68k • written 16 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 16 months ago by 68k • written 16 months ago by ▴ 10
1
vote
3
replies
955
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: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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