User: Lucas Carey

gravatar for Lucas Carey
Lucas Carey40
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5 months, 2 weeks ago
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9 years, 5 months ago
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l**********@gmail.com

Posts by Lucas Carey

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Answer: C: tximport: kallisto .h5 files not recognized as such when they have a different n
... Always something about posting to a forum that makes me find an answer.  This works, but is messy:  1. load the function read_kallisto_h5() from tximport helper.R 2. set importer=read_kallisto_h5 data <- tximport( 'ES_1_high_28881_CGATGT_abundance.h5' , type = "kallisto", txOut = FALSE , tx ...
written 5 months ago by Lucas Carey40
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tximport: kallisto .h5 files not recognized as such when they have a different name
... I have a kalliso-created abundance.h5 file but the filename (ES_1_high_28881_CGATGT_abundance.h5) includes information about the sample. When I try to import this file using tximport v1.10.0 I get an error. tximport thinks that the file is a .tsv file.  However, if I create a symlink named abundanc ...
tximport kallisto written 5 months ago by Lucas Carey40 • updated 5 months ago by Gordon Smyth37k
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Comment: C: what is the best way to get scores for matches from matchPWM() ?
... Hi Patrick, Thanks. Your method, with starting.at = start(hits) brings the function (in a small test case) from 6sec down to 1sec. -Lucas On Jan 20, 2010, at 1:56 PM, Patrick Aboyoun wrote: > Lucas, > Your e-mail was very timely since I just had my hands in the matchPWM code in BioC 2.6. > ...
written 9.4 years ago by Lucas Carey40
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what is the best way to get scores for matches from matchPWM() ?
... Hi All, I'm wondering what is the best way to get the score for every match from matchPWM() in Biostrings Right now, to score all matches to pwm in genome I do this: #Find PWM hits for fwd & reverse complement of PWM for all chromosomes in genome mmf <- sapply(1:Nchr, function(chr){matchPWM ...
written 9.4 years ago by Lucas Carey40 • updated 9.4 years ago by Patrick Aboyoun1.6k

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Popular Question 9.4 years ago, created a question with more than 1,000 views. For what is the best way to get scores for matches from matchPWM() ?

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