Bioconductor Shrna

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edgeR processamplicons shrna

updated 9.0 years ago by thomas.leete • 0 • written 9.2 years ago by Anne Deslattes Mays ▴ 10

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shrna edger deseq2 differential expression normalized counts

8.4 years ago Jane Merlevede ▴ 90

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limma gmap shRNA dropout screen

updated 8.5 years ago by Aaron Lun ★ 28k • written 8.5 years ago by Anna Dvorkin ▴ 40

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edger shrna

7.8 years ago sirintra ▴ 10

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shRNAseq edgeR shRNA

updated 9.2 years ago by Gordon Smyth 52k • written 9.2 years ago by KB ▴ 50

5 results • Page 1 of 1

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Comment: lfcShrink and alpha value by cropero • 0

Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…

Comment: pathview - multiple states by Philippine • 0

Thank you! Here a subset of genes that really works with "ame04145". data <- data.frame( EntrezID = c(100577548, 100577764, 406…

Comment: pathview - multiple states by Guido Hooiveld ★ 4.1k

A quick comment after I copied/pasted your code: when using `geneList1` in the 3rd code chunk I do **not** get a nice plot... I rather got …

Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Adam • 0

Hi Aaron, Thanks a lot for your help! As you mentioned, I checked my data and it is "DelayedMatrix". I don't know the detailed differe…

Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k

You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…

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Answer: contrast matrix design for a continuous variable

A: What's the difference between p.adjust and qvalue?

Answer: DESeq2- merging technical vs biological replicates

Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

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Popular Question to Ou, Jianhong ★ 1.3k