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2
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774
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Is there a function that takes an amino acid string and returns all biologically possible substitutions?
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Student
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14 months ago ronin • 0
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13
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2.1k
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When doing differential methylation using the sesame package, seems to only go one way
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updated 14 months ago by ▴ 20 • written 14 months ago by ▴ 10
17
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How to use removeBatchEffect for removing effect of multiple confounding variables
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updated 14 months ago by 68k • written 9.5 years ago by ▴ 10
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510
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Trying to understand basic DiffBind usage
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14 months ago Alejandro • 0
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892
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modelGeneVar in MulticoreParam: wrong args for environment subassignment
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14 months ago zr • 0
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
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updated 14 months ago by 43k • written 14 months ago by • 0
0
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1
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642
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QSEA:Error in h(simpleError(msg, call))
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14 months ago kf • 0
2
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1
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742
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Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
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updated 14 months ago by 68k • written 14 months ago by ▴ 20
7
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9
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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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updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
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Mark seleced variables in the x-loading plot
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14 months ago Ragnhild • 0
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14 months ago info ▴ 10
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object 'hdac_targets' not found
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1
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2
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844
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14 months ago • updated 13 months ago Arindam ▴ 80
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Issue Installing Biostrings Package: gcc Compilation Errors
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updated 14 months ago by ▴ 70 • written 14 months ago by • 0
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In the sesame package, what does the estimate output mean from testEnrichment()
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15 months ago • updated 14 months ago ramiro.barrantes ▴ 10
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1
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630
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WGCNA Choosing soft threshold power below R^2 0.8
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WARNING: No Bioconductor dependencies detected.
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15 months ago Maria Doyle ▴ 110
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Ideal approach to adjust for covariates for WGCNA
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Help with design matrix for RNA-seq data using edgeR
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
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Problem merging metadata and feature-table before analysing LEfSe on R
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How to use compareCluster in ClusterProfiler?
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question about gseGO() in clusterprofiler package
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updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
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Z-score Interpretation across components
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15 months ago GJ • 0
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error for the geneGOEnricher function of the NoRCE package
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updated 15 months ago by 68k • written 15 months ago by • 0
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Review process for delivering R packages
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15 months ago XFWu • 0
46,691 results • Page 16 of 934
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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…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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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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