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biomaRt connection sql

updated 3.8 years ago by Joan Miró ▴ 80 • written 3.8 years ago by Anand ▴ 10

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MakeOrgPackageFromNCBI NCBI SQL AnnotationForge

updated 4.9 years ago by James W. MacDonald 68k • written 4.9 years ago by chefer • 0

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R shell Python SQL Job

7.2 years ago ematsen ▴ 20

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biomedical informatics data science python SQL Job

9.2 years ago Doe, Aimee ▴ 40

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Answer: Model performance for spline modelling of RNA-seq timecourses in edgeR by Gordon Smyth 52k

I don't understand your question, because there is no difference between limma or glmFit or glmQLFit in terms of spline modeling or the tes…

Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0

Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…

Answer: DESeq2 - am I extracting results incorrectly? by James W. MacDonald 68k

If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…

Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0

I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…

Answer: Origin of the labels for the SingleCellMultiModal dataset by ATpoint ★ 4.8k

If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…

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Limma outputs different results for same sample?

Answer: Improving performance of edgeR and limma while adjusting for multiple confounder

Comment: DESeq - help with pair wise comparisons

Answer: Is random access by row index possible for an indexed VCF file?

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