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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:
3 days, 6 hours ago
Joined:
4 years, 3 months ago
Email:
t************@gmail.com

Posts by Thomas Carroll

<prev • 94 results • page 1 of 10 • next >
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Comment: C: ChIPQC ERROR with "subscript out of bounds"
... hi, I am unable to see some portions of your post. Would it be possible to supply code and session information? best, tom ...
written 11 days ago by Thomas Carroll • 400
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Answer: A: ChIPQC error: NCList object is too deep
... hi Nik, Sorry, this was fixed in release and not in development branch. I have fixed in release and development last night and it should be available in release version 1.18.1 now. best, tom ...
written 11 days ago by Thomas Carroll • 400
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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 4 months ago by Thomas Carroll • 400
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Comment: C: ChIPQC: error during annotation compilation
... hi Herve, Thank you for editing the error message.  tom   ...
written 5 months ago by Thomas Carroll • 400
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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 5 months ago by Thomas Carroll • 400
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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 5 months ago by Thomas Carroll • 400
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Comment: C: ChipQC not loading files
... hi Anna, Did you try moving to DiffBind_Vignette directory? tom ...
written 5 months ago by Thomas Carroll • 400
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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 5 months ago by Thomas Carroll • 400
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Comment: C: ChipQC not loading files
... I guess this is solved for problem in example and can be closed ...
written 5 months ago by Thomas Carroll • 400
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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 6 months ago by Thomas Carroll • 400

Latest awards to Thomas Carroll

Scholar 19 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 20 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 22 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 3.0 years ago, created an answer that has been accepted. For A: ChIPQC and broadPeak input
Scholar 3.0 years ago, created an answer that has been accepted. For A: shiftApply verbosity (in ChIPQC)
Scholar 3.0 years ago, created an answer that has been accepted. For A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
Scholar 3.0 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 3.0 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 3.3 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 3.8 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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