User: Robert M. Flight

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Posts by Robert M. Flight

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Best way to subset one IRanges by list of IRanges
... Is https://github.com/Bioconductor/IRanges the right place to submit any pull requests with the above mentioned method? And it's probably best to continue this conversation there on an issue .... ...
written 10 weeks ago by Robert M. Flight280
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Comment: C: Best way to subset one IRanges by list of IRanges
... I think the arguments are correct, at least based on how I'm currently doing it. If you think of the list wise operation, it becomes: q_by_list = lapply(slist, function(s_sub){ subsetByOverlaps(query, s_sub) }) is what I'm trying to achieve, where each entry in `q_by_list` is the t ...
written 10 weeks ago by Robert M. Flight280
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Comment: C: Best way to subset one IRanges by list of IRanges
... I'm using raw `IRanges` functions to work on raw data points within an mass spectrum. The splitting into lists is to make it easier to do `bplapply` and `furrr::future_map` operations on the subsets of raw data points. So there is definitely no separate spaces like chromosomes in this type of applic ...
written 10 weeks ago by Robert M. Flight280
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Comment: C: Best way to subset one IRanges by list of IRanges
... I will also add, that if I do: query <- IRanges(c(1, 4, 9), c(5, 7, 10)) subject <- IRanges(c(2, 2, 10), c(2, 3, 12)) spartition <- factor(c("a","b","c")) slist <- split(subject, spartition) qlist <- split(query, rep(1, 3)) sublist2 <- IRanges::subsetB ...
written 10 weeks ago by Robert M. Flight280
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Best way to subset one IRanges by list of IRanges
... I have a case where I really want to generate a `list` of subsetted `IRanges` objects, where each one is the result of querying from a `list` of other `IRanges` objects. query <- IRanges(c(1, 4, 9), c(5, 7, 10)) subject <- IRanges(c(2, 2, 10), c(2, 3, 12)) spartition <- fa ...
iranges written 10 weeks ago by Robert M. Flight280
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Comment: C: RCytoscape using Cytoscape v3 REST interface?
... Good to know. So I should wait another Bioconductor release before looking for it as a dependency for my own package? ...
written 4.5 years ago by Robert M. Flight280 • updated 4.5 years ago by Dan Tenenbaum8.2k
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RCytoscape using Cytoscape v3 REST interface?
... Are there any plans to convert the RCytoscape package to use the REST interface in Cytoscape v3? There is an interesting proof of concept post from the Ideker lab now on Github here https://github.com/idekerlab/cy-rest-R ...
rcytoscape written 4.5 years ago by Robert M. Flight280 • updated 4.5 years ago by Dan Tenenbaum8.2k
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subreddit for R related stuff
... Thought there might be some Redditors lurking on these mailing lists. I created a sub-reddit for R (and by extension Bioconductor) discussions, links, etc. http://www.reddit.com/r/Rsoftware/ This will be the first and only shameless plug. -Robert Robert M. Flight, Ph.D. University of Louisville ...
written 7.6 years ago by Robert M. Flight280
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Comment: C: DESeq vs DEXSeq
... Thanks Simon, that was a really useful explanation of how we might want to go about it. -Robert Robert M. Flight, Ph.D. University of Louisville Bioinformatics Laboratory University of Louisville Louisville, KY PH 502-852-1809 (HSC) PH 502-852-0467 (Belknap) EM robert.flight at louisville.edu EM ...
written 7.7 years ago by Robert M. Flight280
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DESeq vs DEXSeq
... We have a biological system where we are interested in finding differential expressed exons (on a genome basis) between conditions, and are wondering whether it is more appropriate to use DESeq or DEXSeq for the analysis. Have RNASeq data on three conditions. >From my understanding of the two pa ...
rnaseq annotation deseq dexseq written 7.7 years ago by Robert M. Flight280 • updated 7.7 years ago by Simon Anders3.6k

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Popular Question 4.5 years ago, created a question with more than 1,000 views. For "romer"ing and "roast"ing around gene sets
Popular Question 4.5 years ago, created a question with more than 1,000 views. For "romer"ing and "roast"ing around gene sets

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