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7
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574
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readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
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CAGEr bug report: wrong consensus cluster results
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error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
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BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
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overlapsAny for elements in GRangesList
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Adding a group of samples reduces DEGs in other groups
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Packages don't update, but no error or warning is thrown
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3 months ago • updated 11 weeks ago gernophil • 0
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With DESeq2 "Not full rank" Error with design ~ line + time + condition
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WGCNA coupled with differential expression analysis: question about baseline module detection
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News: Bioconductor 3.18 is Released!
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limma output for epic array methylation data
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8 months ago Jitendra ▴ 10
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ASpli checks fail on Linux due to missing dependency to statmod
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updated 9 months ago by 50k • written 9 months ago by ▴ 10
5
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create COMPOUND dataset (2 matrices) with rhdf5?
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3 months ago baptiste ▴ 20
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Limma design with continuous and categorical covariates
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updated 13 days ago by • 0 • written 7.7 years ago by ▴ 30
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Cross-species RNA-seq with DESeq2
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updated 10 months ago by 65k • written 6.8 years ago by ▴ 10
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ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
7 months ago Federico ▴ 10
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 4 days ago by 65k • written 2.3 years ago by • 0
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Cannot download GEOmetadb sqlite file
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Not fully paired differential gene expression analysis
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DataFrame Construction With Non-standard Column
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different number of DEG because of outliers
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limma: More differentially expressed genes when factor included in model than when used as blocking factor
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Problem about picking soft threshold power in WGCNA software
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threshold to filter lowly expressed genes
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Confusion about LFC using contrasts weights in EdgeR
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11 weeks ago • updated 10 weeks ago pl23 • 0
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DEG Filtering
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updated 5 weeks ago by 50k • written 7 weeks ago by • 0
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Support for new Illumina human methylation EPIC array v2
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outdated GEOmetadb.sqlite
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14 months ago • updated 3 months ago Robert Castelo ★ 3.3k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
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Differential protein/biomarker expression using limma: is that possible?
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updated 3 months ago by • 0 • written 3.1 years ago by ▴ 10
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Getting rs ids using chr coordinates | Biomart
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Can the limma package be applied to Log2 RUV-normalized data?
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Install DESeq2 problem for macbook pro M1 Max
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
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updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 50
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edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
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updated 8 months ago by • 0 • written 6.5 years ago by ▴ 10
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limma models out of memory issue on Slurm HPC
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updated 4 weeks ago by 50k • written 6 weeks ago by ▴ 10
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Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
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6 months ago • updated 5 months ago kjngo ▴ 40
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updated 19 days ago by 50k • written 7 months ago by ▴ 10
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DiffBind GreyListChIP error: Error: BiocParallel errors
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updated 9 months ago by • 0 • written 2.8 years ago by ▴ 10
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Filter genes by expression for voomLmFit
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updated 5 months ago by 50k • written 5 months ago by • 0
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Light difference when using coef vs omit a group when compare 3 groups.
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26 days ago • updated 18 days ago Chris • 0
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2
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can't install DESeq2 ("unable to access index for repository")
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8 months ago Alessia ▴ 40
5
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Archive location for Bioconductor packages
archive
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PhD student
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10 months ago Nisha • 0
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11
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Visualization of negative log CPM values
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written 11 months ago by ▴ 20
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How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by • 0
4
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7
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should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 7.9 years ago by • 0
4
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3
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catchSalmon for tx-level DE
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updated 5 months ago by 50k • written 3.5 years ago by ★ 4.1k
1,000 results • Page 2 of 20
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
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Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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