User: Bioinformatist Newbie

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Posts by Bioinformatist Newbie

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Comment: C: How to interpret DNAShapeR results
... @tsupeich Does it make sense to take average of all the individual  (1 neucletide resolution) features e.g. MGW.1 ... MGW.200 ? Isn't it that we loose the information content of true TF binding sites by taking average of feature value across the entire width of the given sequence (e.g. 200 in this c ...
written 3.3 years ago by Bioinformatist Newbie0
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How to interpret DNAShapeR results
... Hello, I have to compute DNA shape features (MGW, Roll, ProT, HelT) for genomic ranges of my interest. My GRanges object is something like: > head(gr) GRanges object with 6 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> < ...
dnashaper written 3.3 years ago by Bioinformatist Newbie0 • updated 3.3 years ago by tsupeich30
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Differential Expression Analyses of Entire Connectivity Map (microarray) dataset
... Hi, I am interested in finding the differentially expressed genes among all instances of Connectivity Map dataset. CMAP dataset contains a collection of gene expression profiles (6100 instances) that are obtained from cultured human cells treated with various small molecules (approx. 1300). Two kin ...

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