Showing : rnaseq • reset
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 1 day ago by 53k • written 1 day ago by • 0
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2.9k
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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
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9
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613
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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
4 weeks ago mohammedtoufiq91 ▴ 10
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8
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476
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
5 weeks ago Jiahao Tian • 0
3
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11
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1.8k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 11 months ago by • 0
3
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2
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762
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
7 weeks ago mohammedtoufiq91 ▴ 10
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5
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694
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WGCNA
WGCNA Normalization RNASeq
written 6 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 3 months ago by ▴ 20
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1
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452
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 3 months ago by 43k • written 4 months ago by • 0
2
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5
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1.2k
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Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 3 months ago by ▴ 110 • written 3 months ago by ▴ 10
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209
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Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
3 months ago dudwnsrla1 • 0
2
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6
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2.9k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
4 months ago • updated 3 months ago massimo • 0
1
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1
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1.2k
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 5 months ago by ★ 4.9k • written 5 months ago by • 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 5 months ago by • 0
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0
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389
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
6 months ago GT • 0
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3
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830
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 6 months ago by 43k • written 6 months ago by • 0
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2
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1.3k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 7 months ago by ★ 4.9k • written 7 months ago by • 0
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1
reply
330
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 7 months ago by 43k • written 7 months ago by • 0
0
votes
3
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761
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 7 months ago by • 0 • written 7 months ago by ▴ 10
0
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1
reply
459
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
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2
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781
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
7 months ago ingrid.h • 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
7 months ago Quang NN ▴ 10
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3
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822
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 8 months ago by • 0
4
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2
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915
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 9 months ago by ★ 4.9k • written 9 months ago by ▴ 10
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5
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906
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Deseq2 Design
RNASeq DESeq2
updated 9 months ago by 68k • written 9 months ago by • 0
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2
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815
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 9 months ago by 53k • written 9 months ago by ▴ 10
0
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1
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553
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 9 months ago by ★ 4.9k • written 9 months ago by • 0
1
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5
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1.0k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 9 months ago by • 0
0
votes
1
reply
372
views
eRNAs count
RNASeq DESeq2
updated 9 months ago by ★ 4.9k • written 9 months ago by • 0
1
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8
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2.3k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 10 months ago by • 0
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0
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346
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
10 months ago brayas13 • 0
2
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4
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793
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
11 months ago jihoon.kim.1495 ▴ 10
1
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1
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907
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 11 months ago by 68k • written 11 months ago by • 0
1
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2
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805
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 11 months ago by 43k • written 11 months ago by ▴ 10
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3
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988
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
11 months ago Travis • 0
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5
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2.2k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.3 years ago by • 0
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2
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1.5k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
3
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5
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2.2k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
2
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3
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1.1k
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
13 months ago BioinfGuru ▴ 70
3
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6
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1.2k
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 13 months ago by • 0
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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
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3
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895
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
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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
14 months ago • updated 13 months ago Lucy ▴ 60
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4
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995
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 14 months ago by • 0
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0
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644
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
14 months ago JG13 • 0
0
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1
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620
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 15 months ago by 68k • written 15 months ago by • 0
1
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9
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3.0k
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 15 months ago by ▴ 10
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3
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915
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 15 months ago by 68k • written 15 months ago by ▴ 50
2
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2
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948
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 15 months ago by ▴ 10 • written 16 months ago by • 0
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6
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2.1k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
15 months ago atan • 0
1,407 results • Page 1 of 29
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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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