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15k
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deseq2 timecourse
updated 4 months ago by 43k • written 9.8 years ago by ▴ 130
34
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30
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deseq2 filter the low counts
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updated 12 months ago by • 0 • written 9.9 years ago by ▴ 40
17
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updated 3 months ago by 67k • written 8.6 years ago by ▴ 10
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remove microarray batch effects using Limma
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updated 9 months ago by • 0 • written 6.0 years ago by 4.1k
16
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Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 4 months ago by • 0 • written 8.8 years ago by ▴ 60
15
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Why p value inconsistent when using different number of pathway score?
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8 months ago Chris ▴ 20
15
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23
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The difference when using Limma compare between 3 conditions vs 2 conditions
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DESEq2 Paired samples Before and after treatment
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12
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Rsamtools is not available for (for R version 4.0.2)
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updated 5 months ago by • 0 • written 4.5 years ago by ▴ 40
12
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GSEA many significant gene sets despite no differentially expressed genes
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updated 11 months ago by ★ 4.6k • written 2.8 years ago by ▴ 70
12
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updated 8 months ago by • 0 • written 9.8 years ago by ▴ 150
10
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11
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 7 months ago by • 0 • written 7.4 years ago by ▴ 80
10
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22k
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Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
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updated 3 months ago by 67k • written 5.6 years ago by ▴ 30
10
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Ensembl plants at annotationHub?
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updated 7 months ago by • 0 • written 6.1 years ago by ★ 4.1k
10
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7
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Why in Bioconductor community people rarely upvote questions?
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updated 9 weeks ago by 4.1k • written 23 months ago by ▴ 50
9
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Where can I find EnsDb.Hsapiens.v105?
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updated 6 months ago by 4.1k • written 3.0 years ago by ▴ 40
9
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38
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manipulate bedpe format files
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12
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updated 9 months ago by • 0 • written 9.5 years ago by ▴ 30
8
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921
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DGE analysis with LIMMA
limma
updated 10 months ago by 52k • written 10 months ago by • 0
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12
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DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)
DEXSeq
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8
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3
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Appropriate ways to filter counts data for voom/limma
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Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
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updated 7 months ago by ▴ 30 • written 5.7 years ago by ▴ 160
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updated 9 months ago by ★ 3.4k • written 9 months ago by ▴ 50
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updated 5 months ago by 43k • written 4.4 years ago by ▴ 40
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clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
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biomaRt server error, and mirrors do not help
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wgcna
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7
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3
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limma::voom vs edgeR::voomLmFit - when to use?
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16
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updated 11 months ago by 52k • written 9.8 years ago by ★ 7.9k
7
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903
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ANOVA like approach of edgeR
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Batch Effect Correction, Gene Filtering
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updated 9 months ago by 52k • written 9 months ago by • 0
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limma plotMDS - logFC inverted?
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How to properly average normalized counts of biological replicates
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findOverlaps(), queryHits and subjectHits()
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updated 5 weeks ago by ★ 4.6k • written 6 weeks ago by ▴ 10
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readDGE in edgeR giving me path names as sample names
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updated 11 months ago by 52k • written 11 months ago by • 0
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 6 days ago by 67k • written 12 days ago by • 0
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10
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overlapsAny for elements in GRangesList
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updated 9 months ago by • 0 • written 8.7 years ago by ▴ 180
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BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
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14 months ago • updated 8 months ago shepherl 4.1k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 10 weeks ago by 52k • written 9 months ago by ▴ 50
6
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 8 days ago by ▴ 20 • written 4 months ago by • 0
1,460 results • Page 1 of 30
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
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Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
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