1
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6
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1.8k
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low counts from microRNA seq
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3.1 years ago abhay.kanodia • 0
3
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1
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1.3k
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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2
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Cannot install packages in R/BiocManager_Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TR…
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updated 3.1 years ago by 68k • written 3.1 years ago by • 0
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1
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2.1k
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topGo error loading data
topGO GO
3.1 years ago peter • 0
0
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2
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DESeq2: overlap differentially expressed genes with and without interaction term
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3.1 years ago xuscha • 0
1
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1
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1.1k
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Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 3.1 years ago by ★ 1.3k • written 3.1 years ago by ▴ 10
2
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2
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Inccorect group number in DGEList
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updated 3.1 years ago by 53k • written 3.1 years ago by • 0
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2
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clusterProfiler - custom annotations
clusterProfiler
updated 2.0 years ago by ★ 4.1k • written 3.1 years ago by • 0
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2
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Memory error when trying to read part of H5 file
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updated 3.0 years ago by ★ 6.6k • written 3.1 years ago by • 0
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3
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Error in SummarizedExperiment in DESeq2
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3.1 years ago Cherif • 0
0
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3
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DESeq2 Statistic - Padj NA
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updated 3.1 years ago by 43k • written 3.1 years ago by • 0
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How can I limit the number of displayed genes in heatplot
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updated 2.4 years ago by • 0 • written 3.1 years ago by • 0
0
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0
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865
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Installing edgeR on M1 mac
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3.1 years ago Onur • 0
0
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1
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1.5k
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DeSeq2 and GenomicRange installation possible conflict with bioconductor version 3.16?
DESeq2 version3.16 installation bioconductor GenomicRange
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
1
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1
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4.5k
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packages not installing from sources the package which needs compilation
Install
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
4
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6
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recount 3 protect read length metadata
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updated 3.0 years ago by ★ 1.1k • written 3.1 years ago by ▴ 20
1
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1
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2.1k
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How to include background "universe" in compareCluster function of clusterprofiler package
clusterProfiler
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
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2
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918
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I need help with EdgeR!
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updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
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0
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Problems running WGCNA
WGCNA
3.1 years ago S • 0
0
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2
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1.4k
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Errors estimating cell types using DNA methylation cord blood reference data
FlowSorted.Blood.EPIC
3.1 years ago metamaden ▴ 10
0
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0
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1.1k
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ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
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3.1 years ago cwarden45 • 0
0
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0
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757
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Missing region location database for mm10 in the package
RcisTarget
3.1 years ago Isabelle Stévant ▴ 10
0
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0
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694
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benchdamic 1.4.0 fitNM matrix input
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3.1 years ago Robert Dunne ▴ 10
0
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7
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4.4k
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msa: object 'msaClustalW' of mode 'function' was not found
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updated 3.1 years ago by ▴ 300 • written 5.4 years ago by • 0
1
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2
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2.4k
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running DESeq2 from nanopore wf-alignment workflow
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updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1
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7
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Adding geneID to list of gene locus IDs
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written 3.2 years ago by • 0
0
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3
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1.9k
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Representation of self-loops and the calculation of degrees
graph
updated 2.3 years ago by 6.7k • written 3.1 years ago by • 0
0
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1
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2.1k
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Trying to generate a pd file for ChAMP from idat files with no array or slide information in file names
ChAMP
updated 3.1 years ago by 68k • written 3.1 years ago by ▴ 10
3
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4
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3.3k
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RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
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3.1 years ago • updated 3.0 years ago spg • 0
0
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1
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DiffBind: Error in pv$called[, mask] : subscript out of bounds
DiffBind
updated 3.1 years ago by ★ 5.2k • written 3.2 years ago by • 0
0
votes
1
reply
1.0k
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[Methylkit]-Error in validObject(.Object) :
methRead methylkit
3.1 years ago liulip • 0
0
votes
2
replies
1.5k
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Analyzing barcode sequencing experiments with DESeq2/edgeR
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updated 3.1 years ago by • 0 • written 3.6 years ago by • 0
0
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2
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TnSeq as ZINB? Alternatives in R?
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updated 3.1 years ago by • 0 • written 3.2 years ago by ▴ 90
2
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1
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1.2k
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limma: R-squared for time-series data
limma
updated 3.1 years ago by 53k • written 3.1 years ago by ★ 5.0k
1
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4
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Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
OrgDb
3.1 years ago hendrikwenneker ▴ 10
1
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2
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1.2k
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DiffBind Loss and Gain location
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updated 3.0 years ago by ★ 5.2k • written 3.1 years ago by • 0
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0
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548
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A problem with Experimental Design for Limma
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3.1 years ago ToReality • 0
1
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3
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Convert Chromosome postion to gene symbol
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3.1 years ago mbansal • 0
5
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10
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lpsymphony compilation trouble
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updated 3.1 years ago by ★ 6.6k • written 7.9 years ago by ▴ 40
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3
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Unusual MA and volcano plots?
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written 3.1 years ago by ▴ 10
2
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4
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question regarding installation of "enrichplot" with BiocManager
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written 3.2 years ago by • 0
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4
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CoGAPS Installation Problem - clang compiler does not support '-march=native'
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3.1 years ago • updated 3.0 years ago MayerAdam • 0
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2
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suggestions/comments on DESeq transcript wise analysis
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written 14.0 years ago by ▴ 190
0
votes
0
replies
832
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normFactors or calcNormFactors (computing the normalization or scaling factors)
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3.1 years ago Bogdan ▴ 670
0
votes
1
reply
689
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How does DESeq2 handle multiple conditions in one design.
DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
1
reply
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Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
2
replies
915
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NanoStringDiff contrast vectors
NanoStringDiff
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
1
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0
replies
996
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News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
3.1 years ago Levi Waldron ★ 1.1k
0
votes
1
reply
938
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Using DESeq2 for time-series analysis with two conditions
DESeq2 RNASeqData
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
3
votes
6
replies
1.9k
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
3.1 years ago mohammedtoufiq91 ▴ 10
46,730 results • Page 68 of 935
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Comment: Upcoming Ensembl API and data access changes - new blog post available by Hugo Gruson • 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
Comment: Are individual-mouse-based statistics possible in CellChat? by LillianaVolkman99 • 0
thank you very much. https://www.biostars.org/p/9617271/
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
My apologies, I forgot that `design.group` is not included in the final matrix, because the baseline group effects are already captured by …
Answer: Bile acid analysis with limpa by Gordon Smyth 53k
I am not familiar with targeted HPLC-MS and I don't know what you mean by "peak areas". If it produces standard format mass spec data from …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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