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1
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How to get similarity score between two genomes of different species
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5.3 years ago drew.neely • 0
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1
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Does SingleR return output for every cell it's given or only those that it can provide an annotation for?
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853
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In edgeR, how am I supposed to be gauging the results of the BCV Plots, the values of common dispersion, tagwise disperson, ect.
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2
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DESeq2 # of up-and down-regulated genes are approximately equal
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updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
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1
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DEseq2 data format
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5
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R, minfi, remove probes from RG channel set (S4 object, DNA methylation array data)
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1
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1
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1.2k
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Is it possible to run arrayQualitymetrics or some similar package on a HTAFeatureSet?
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updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
3
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4
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Is it possible to run DMRcate directly with genomic positions instead of probe names?
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1
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1.5k
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Vignette Run Time
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updated 5.3 years ago by 25k • written 5.3 years ago by ▴ 10
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5.3 years ago dh.heredero ▴ 10
0
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3
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2
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6
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How to get results from random intercepts using the limma package?
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updated 5.3 years ago by 53k • written 5.3 years ago by ▴ 10
0
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3
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updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
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11
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how to deal with differential analysis between 3 groups in DESeq2?
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updated 5.3 years ago by ★ 1.4k • written 5.3 years ago by • 0
2
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13
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updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
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1
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1
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589
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DESeq2 contrasts and their interpretation
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updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
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padj NA after shrinking log2FC (DESeq2)
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5.3 years ago da.de ▴ 30
0
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1
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748
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updated 5.3 years ago by 43k • written 5.3 years ago by • 0
3
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News: List of Deprecated Packages for Bioc3.12
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5.4 years ago • updated 5.3 years ago shepherl 4.3k
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Job: Scientific Computing Team Leader
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analysis of FACS data using BioC
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RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
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DESeq on tissue mixing experiment
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Discarding ambient RNA using estimateAmbience
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updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 50
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is there an R library to compute semantic similarity in SNOMED ontology?
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updated 5.3 years ago by 6.7k • written 5.3 years ago by • 0
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Limma Design Matrix Missing Columns
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5.3 years ago He Huang • 0
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2
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Reasoning behind weighting of of exon expression values in limma diffSplice function
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updated 5.3 years ago by 53k • written 5.3 years ago by • 0
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How to create geneselectionfunction in TopGO: Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector
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R: Find all genes associated with a genomic range
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updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 10
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News: New Package Submission Deadline for Bioc Release 3.12
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5.3 years ago shepherl 4.3k
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DESeq2 fitType question
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1
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Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
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updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
3
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2
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updated 5.3 years ago by 1.6k • written 5.3 years ago by • 0
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DESeq2: Variables in the design section
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updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 60
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Job: developer/project management position at Harvard Medical School
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How to add colors to the PCA made using SNPRelate
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updated 5.3 years ago by 68k • written 5.3 years ago by • 0
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2
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updated 5.3 years ago by 25k • written 5.3 years ago by • 0
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0
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Probe Design questions
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5.3 years ago henry1995910343 • 0
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1
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1.2k
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library(rDGIdb) and Error in curl
DGIdb
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
0
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3
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getSRA() from the SRAdb package is returning an empty data.frame from the full SQL file, but not the demo file
SRAdb getSRA()
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
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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 …
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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 …
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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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Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
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