User: t.candelli

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t.candelli60
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France
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3 years, 1 month ago
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Posts by t.candelli

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Conditional motif enrichment in sequence and selex data
... hey Vincent, thanks for your answer. by "other sequences" i actually meant motif XXXX, although it can easily be extended to motif YYYY. what i mean is that the process of selection itself (independently of what it selects) is going to change the nucleotide frequency. therefore comparing the frequen ...
written 3.9 years ago by t.candelli60
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Conditional motif enrichment in sequence and selex data
... I am working with sequence data and want to determine the enrichment of flanking nucleotides of a motif. let XXXX be the motif i'm interested in. i want to know if, for example, (A|XXXX) is enriched or not over the background. to do this i took the frequency of (A|XXXX) and compared it to the freq ...
enrichment selex motif conditional probability written 3.9 years ago by t.candelli60
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Comment: C: PAR-clip T to C mutations becoming T to G in minus strand?
... yeah i thought a long while about this and realized that in SAM files the sequence is always given on the forward strand, irrespective of whether it maps to the reverse. this flipping makes it so the T->C in the reverse become A->G in the forward. i am relatively convinced by this but i would ...
written 4.7 years ago by t.candelli60
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PAR-clip T to C mutations becoming T to G in minus strand?
... I am looking at some PAR-clip data. trimming and mapping went perfectly, however, when i look at the data on IGV, in the plus strand i have a vast majority of T to C mutations (as expected), but in the minus strand i see a lot of T to G mutations, like a vast predominance. is there any way to expla ...
par-clip transversion mapping igv written 4.7 years ago by t.candelli60 • updated 4.7 years ago by Istvan Albert ♦♦ 80k
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Comment: C: How to keep my data and analysis up to date across new genome releases
... UCSC does publish a number of "diffs", or in this context chain files, between a number of different assemblies in different organisms here. i will update the answer to be more detailed. ...
written 5.1 years ago by t.candelli60
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Answer: A: How to keep my data and analysis up to date across new genome releases
... It depends on which kind of analysis you do. if your outputs are simple data representation such as .bed or .bedgraph files the liftOver tool from UCSC can help keep everything up to date. it might require more work in generating the chain files if you work with unusual organisms. this method works ...
written 5.1 years ago by t.candelli60
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Comment: C: Loop with 2 levels in R
... correct, sorry i edited the answer   ...
written 5.1 years ago by t.candelli60
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Comment: C: Determine differential expression for microarray data; sample size = 2 + many te
... one possibility is to manually average the technical replicates and use only the biological replicates to perform the statistical tests. This review suggests this course of action. The alternative is to mix technical and biological replicates, but it does not seem like a solid answer. also, pairing ...
written 5.1 years ago by t.candelli60
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Answer: A: plotting interactions in R with two data sets
... i'm going to use the "pheatmap" package to draw a heatmap of your data. with the code below i generate a matrix from your dataframe so that it can be used as an argument for pheatmap.   library(pheatmap)   names<-unique(c(data[,1], data[,2])) mat<-matrix(data=0, nrow=length(names), ncol=le ...
written 5.2 years ago by t.candelli60
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Comment: C: plotting interactions in R with two data sets
... i think the best way to represent this sort of data would be with a heatmap. is there a directionality between partner one and partner 2? e.g. the values  "1    5000   8" are different from "5000    1    8" in your table ...
written 5.2 years ago by t.candelli60

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Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: How to keep my data and analysis up to date across new genome releases

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