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6
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2.3k
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DESeq2 Normalization with 4 Groups
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2.1 years ago erika.maldonado-rosado • 0
1
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2
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
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written 2.1 years ago by ▴ 10
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2
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How can I devise a method like DESeq2 to give statistics for paired multiple -omic datasets?
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proActiv - Error in estimateSizeFactorsForMatrix when using the proActiv function
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2.1 years ago Chris • 0
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5
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error while running DMRcate
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How to correct for known and surrogate variables in DESeq2?
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updated 20 months ago by 43k • written 2.1 years ago by • 0
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DMR.plot() Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
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updated 2.1 years ago by 4.2k • written 2.1 years ago by • 0
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Problems when running GDC_prepare in R
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2.1 years ago leon • 0
0
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5
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updated 2.0 years ago by 53k • written 2.2 years ago by • 0
0
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MEDIPS - covariate
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updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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2.2 years ago • updated 2.1 years ago Belinda • 0
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Two factor design including interaction effect with DESeq2 in R
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updated 2.1 years ago by ★ 1.4k • written 2.2 years ago by • 0
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Need help generating BSgenome and orgdb
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2.2 years ago • updated 22 months ago mat149 ▴ 80
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1
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rtracklayer error for browserSession UCSC
rtracklayer
updated 2.2 years ago by 16k • written 2.2 years ago by ▴ 10
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Using injectSNPs with a custom set of SNPs
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written 2.2 years ago by • 0
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7
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[Bug] Segfault in edgeR::cpm
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updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ▴ 20
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is Dada2 biased toward a particular sequence ?
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2.2 years ago Sara • 0
0
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2
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DESeq2: how could the lower mean abundance treatment show a positive and significant LFC?
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2.2 years ago • updated 2.1 years ago Roey Angel • 0
0
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4
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Retrieve gene ontologies (GO) for genes and a species by REST API
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2.2 years ago Rockbar • 0
2
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4
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Question about creating custom organism database with AnnotationForge
AnnotationForge
2.2 years ago Adrian • 0
0
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0
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News: COURSE - Developing R/Bioconductor Packages for Genomics
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2.2 years ago info ▴ 10
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2
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Will DESeq2 be appropriate tool for analysis?
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2.2 years ago Karthik • 0
0
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1
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DESeq2 Error in Results Contrast and ResultsNames
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updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
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2
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recount3 monorail pipeline version
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2.2 years ago • updated 24 months ago Lorenzo • 0
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bioNeuro plot_expression_profile - how to order samples in plot output
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2.2 years ago Christopher ▴ 20
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0
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Dual species RNA-seq, Library size and normalization
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2.2 years ago Florian • 0
0
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choosing rank for GSEA
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updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
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0
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Pysam pileup and Rsamtools pileup output discrepancy
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2.2 years ago Xinqi • 0
1
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2
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AnnotationHub data for Mus musculus seems to be missing, while previously it was there
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2.2 years ago Thon • 0
0
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0
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Using DADA2 for finding viral sequence variants
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2.2 years ago Sara • 0
1
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5
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Duplicated expression values?
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written 2.2 years ago by • 0
2
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2
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918
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"Details" section for specific software packages
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edgeR heatmap construction and interpretation
heatmaps
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
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2
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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
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2.2 years ago Benji Bromberg ▴ 30
1
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1
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Multiple comparison using DESeq2
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updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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Tximport Error - transcripts in quant files are not the same as tx2gene
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updated 2.2 years ago by 43k • written 2.2 years ago by • 0
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Subsetting Range Summarized Experiment
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2.2 years ago Bine ▴ 50
0
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0
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726
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How many ancestries to send in admixMap() when doing a two-way analysis?
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2.2 years ago mailtoshivam13 • 0
0
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2
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Using dplyr commands with DataFrame objects
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2.2 years ago GE • 0
0
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4
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News: Important Bioconductor Release 3.18 deadlines this week
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updated 2.2 years ago by ★ 4.1k • written 2.2 years ago by 4.2k
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enrichPlot error when plotting topGO results
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updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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reply
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GenomeInfoDbData version 1.2.9
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updated 2.2 years ago by 4.2k • written 2.2 years ago by • 0
0
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5
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minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
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2.2 years ago dorota.komar • 0
2
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5
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Help with orgdb for non-model species via makeOrgPackageFromNCBI
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updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 80
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Long-read mode in featureCounts
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2.2 years ago mmisak • 0
0
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1
reply
845
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Issue with weights in voomLmFit()
limma
updated 13 months ago by 53k • written 2.2 years ago by ▴ 170
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2
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minfi differential methylation analysis errors
minfi
2.2 years ago matthew.sinton • 0
1
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2
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tximeta error with vroom
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2.2 years ago Pufall, Miles A ▴ 30
2
votes
4
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Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
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2.2 years ago Erica • 0
0
votes
1
reply
1.2k
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Multiple groups comparison using Linnorm
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updated 2.2 years ago by • 0 • written 4.4 years ago by • 0
46,695 results • Page 40 of 934
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
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C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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