User: Thomas Carroll

gravatar for Thomas Carroll
Reputation:
400
Status:
Trusted
Location:
United States/New York/The Rockefeller University
Website:
https://rockefelleruni...
Scholar ID:
Google Scholar Page
Last seen:
2 months, 1 week ago
Joined:
4 years, 1 month ago
Email:
t************@gmail.com

Posts by Thomas Carroll

<prev • 92 results • page 1 of 10 • next >
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Answer: A: ChIPQC: error during annotation compilation
... hi, I have added the fix in development version ChIPQC 1.17.1 and to ChIPQC 1.16.1 now. Should be available from git repository and through biocLite tomorrow. very best, tom ...
written 11 weeks ago by Thomas Carroll400
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Comment: C: ChIPQC: error during annotation compilation
... hi Herve, Thank you for editing the error message.  tom   ...
written 11 weeks ago by Thomas Carroll400
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Answer: A: ChIPQC: error during annotation compilation
...   hi, Thank you for report. Yes, it looks like something changed in behavior of unlist on a GRanges objects. > library(GenomicRanges) > unlist(GRanges("chr1:10-100")) GRanges object with 1 range and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> & ...
written 11 weeks ago by Thomas Carroll400
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Comment: C: ChipQC not loading files
... hi Anna, Do you mind accepting my answer at the top? thank you, tom ...
written 11 weeks ago by Thomas Carroll400
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Comment: C: ChipQC not loading files
... hi Anna, Did you try moving to DiffBind_Vignette directory? tom ...
written 3 months ago by Thomas Carroll400
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Comment: C: ChipQC not loading files
...   hi Anna, As the Dffbind command is not working this suggest the wrong working directory. The CSV you are reading lists files as relative paths from the location inside the Diffbind vignette directory. So reading the CSV will work but it will not be able to find any files unless you are in same ...
written 3 months ago by Thomas Carroll400
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Comment: C: ChipQC not loading files
... I guess this is solved for problem in example and can be closed ...
written 3 months ago by Thomas Carroll400
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Answer: A: ChipQC not loading files
... hi Anna, Your example code is working for me in the versions you are running (version ChIPQC_1.16.0 and Diffbind Version DiffBind_2.8.0). ------------ > setwd("~/../../Volumes/Untitled/DiffBind_Vignette/") > library(ChIPQC) > samples = read.csv(file="tamoxifen.csv") > exampleExp = ChI ...
written 3 months ago by Thomas Carroll400
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Comment: C: ChipQCreport coverage plot failure?
... hi, Would you be able to share the BAM file with me on Box (tc.infomatics@gmail.com) so I can try and find the source of this? best, tom ...
written 4 months ago by Thomas Carroll400
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Comment: C: ChIPQC error: "non-zero exit status"
... Could you post your session information so we can see which versions of libraries you currently have installed? best, tom ...
written 4 months ago by Thomas Carroll400

Latest awards to Thomas Carroll

Scholar 17 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 18 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 18 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 20 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 2.8 years ago, created an answer that has been accepted. For A: ChIPQC and broadPeak input
Scholar 2.8 years ago, created an answer that has been accepted. For A: shiftApply verbosity (in ChIPQC)
Scholar 2.8 years ago, created an answer that has been accepted. For A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
Scholar 2.8 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 2.8 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 3.2 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 3.6 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine

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