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346
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Feedback needed on new user-friendly BED file tool
bedbaser offtopic
updated 3 months ago by 68k • written 3 months ago by • 0
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updated 3 months ago by 68k • written 3 months ago by • 0
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Empty boxes in treemap plot rrvgo package
rrvgo
3 months ago Asma • 0
0
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3
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532
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DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
3 months ago Shajahan • 0
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13
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Highly DE genes but small count difference within conditions
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3
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3 months ago mohammedtoufiq91 ▴ 10
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208
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Results with PON give more variants
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ORFik: spliced 5utr regions
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MEDIPS.meth gives table with NA rpkm values
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updated 3 months ago by 68k • written 3 months ago by • 0
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Using offset in edgeR
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updated 3 months ago by 53k • written 3 months ago by • 0
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ExperimentHub full metadata
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Non-monotonic voomByGroup plot in Xenium data
XeniumIO voom
3 months ago richardallenfriedmanbrooklyn ▴ 30
0
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215
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Guidance Requested on GCN Network Analysis and Module Enrichment in R
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updated 11 weeks ago by 43k • written 3 months ago by • 0
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615
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cytolib uses outdated boost call
cytolib
updated 3 months ago by 68k • written 3 months ago by • 0
4
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8
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Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
3 months ago richardallenfriedmanbrooklyn ▴ 30
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can't post
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updated 3 months ago by 4.2k • written 3 months ago by • 0
7
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competitive enrichment test yields too few significant results, self-contained too many
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3 months ago bbao ▴ 10
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How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
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Install old version of DESeq2
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
3
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Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 8 days ago by • 0 • written 4 months ago by ▴ 10
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Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
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3 months ago Valeria • 0
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4 months ago Wei Shi ★ 3.6k
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Regarding the issue of background genes in enrichment analysis
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Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
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updated 4 months ago by 53k • written 4 months ago by • 0
2
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I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
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4 months ago John ▴ 10
0
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4 months ago Mara • 0
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parameters of filterByExpr
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compute_fasta_digest does not match Salmon index hash
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Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
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ChAMP pipeline error (champ.import)
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updated 4 months ago by • 0 • written 6.6 years ago by • 0
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updated 4 months ago by ★ 5.0k • written 4 months ago by • 0
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updated 3 months ago by 43k • written 5 months ago by • 0
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697
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Which GTF file to use for creation of tx2gene files?
tximport
updated 4 months ago by 43k • written 4 months ago by • 0
1
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
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0
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updated 4 months ago by • 0 • written 4 months ago by • 0
1
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Is voomByGroup available in limma?
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4 months ago richardallenfriedmanbrooklyn ▴ 30
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How to use goana function with zebrafish genome from org.Dr.eg.db
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4 months ago Eric • 0
1
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3
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0
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4 months ago Enfurry 0
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Y-axis break ihn Volcano Plot
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4 months ago rajdeepboral00 • 0
0
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0
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getQC(RGset.raw) from IlluminaHumanMethylationMSAmanifest
getQC hcg110.db
updated 4 months ago by 4.2k • written 4 months ago by • 0
3
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Biological replicates consideration in DESeq2 design formula.
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written 5 months ago by ▴ 20
1,000 results • Page 3 of 20
Recent ...
Replies
Comment: Failure to download resources (MeSHDb) from AnnotationHub by Steve Lianoglou ★ 13k
That fixed it, thanks Lori!
Comment: Suppress warning in RHDF5 write by nicolas.lhuillier • 0
Thanks a lot for the quick and effective reply. I had tried "suppressWarnings" but not "suppressMessages".
Answer: Suppress warning in RHDF5 write by James W. MacDonald 68k
``` > fun <- function() message("this is a message") > fun() this is a message > suppressMessages(fun()) > ```
Answer: Failure to download resources (MeSHDb) from AnnotationHub by shepherl 4.2k
apologies. These are contributed by someone outside the core team. On upload I did not realize they included the older Bioconductor storage…
Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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