Bioconductor Galignments

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rtracklayer Rsamtools GAlignments GRanges metadata

updated 4.5 years ago by Hervé Pagès 16k • written 4.5 years ago by Robert ▴ 10

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deseq2 rnaseq count matrix galignments granges

updated 7.4 years ago by Michael Love 42k • written 7.4 years ago by bananaal1 ▴ 10

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annotation GAlignments bamfileobject renameseqlevels

7.8 years ago teresati ▴ 10

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Rsamtools GAlignments pileup

updated 8.5 years ago by Martin Morgan 25k • written 8.5 years ago by jesper.gadin ▴ 10

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Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di by James W. MacDonald 67k

The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…

Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…

Comment: Identifying potentially associated gene set to drug response using GSVA by Kent • 0

Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…

Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification by James W. MacDonald 67k

You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…

Answer: HilBertVis install error by James W. MacDonald 67k

It appears you have compiler flags set that preclude you from compiling (-Werror=format-security). If I install `HilbertVis` on my work box…

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A: TopGO: How to retrieve the gene list related to a GO ID ?

A: Error in DESeqDataSet : some values in assay are not integers

A: correcting the batch effects in Limma and SVA

A: Using of limma moderated t-test with "corrected" expression matrix resulting fr

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