User: Coby Viner

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Coby Viner50
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University of Toronto, Canada
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cobyviner
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2 years, 2 months ago
Joined:
3 years, 4 months ago
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Posts by Coby Viner

<prev • 24 results • page 1 of 3 • next >
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Comment: C: ChIPQC installation does not force latest DiffBind version
... Hi Tom, Thanks for looking into this! Unfortunately, I did not record that, so I am not entirely sure. I think that it may have been version 2.4.2 (the current system version), but it may have been a much earlier version from a previous installation of mine. -- Coby ...
written 2.4 years ago by Coby Viner50
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ChIPQC installation does not force latest DiffBind version
... Upon installing the latest version of ChIPQC (1.12.1) in a new R 3.4.0 installation, I encountered a few different errors upon running ChIPQCreport. These various errors were all resolved, once I upgraded DiffBind to the latest version (2.4.4). ChIPQC should therefore install the latest available v ...
diffbind chipqc chipqcreport written 2.4 years ago by Coby Viner50 • updated 2.4 years ago by Thomas Carroll400
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Comment: C: ChIPQCreport yields a cryptic error if "Replicate" data is not specified
... Just wanted to follow-up on this. This workaround is still needed in the latest version (1.12.0) and the same cryptic error message is emitted without it. ...
written 2.4 years ago by Coby Viner50
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ChIPQC with GRCh38/hg38 requires manual loading of hg38 annotation
... While ChIPQC can now function on GRCh38/hg38, via annotation="hg38", it requires manual loading of TxDb.Hsapiens.UCSC.hg38.knownGene. This package should be loaded as a dependency, as with other annotations. ...
chipqc written 2.4 years ago by Coby Viner50 • updated 2.4 years ago by Thomas Carroll400
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ChIPQC comparison of controls - uniqueness error
... I am trying to compare different controls for various ChIP-seq datasets. Accordingly, I have experiments with the same BAM experiment file (bamReads), but with different control BAM files (bamControl). Therefore, I have multiple sample lines with the same bamReads, but different bamControl values. ...
chipqc written 2.5 years ago by Coby Viner50
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ChIPQC plotSSD adds a legend even without a blacklist [minor]
... ChIPQC's plotSSD results in a figure including a legend with both "Pre_Blacklist" and "Post_Blacklist" legend labels, with a non-existent handle for the latter, when no blacklist is provided. Ideally, the legend should simply be disabled in such cases. ...
chipqc written 3.1 years ago by Coby Viner50
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Comment: C: ChIPQCreport yields a cryptic error if "Replicate" data is not specified
... I appreciate this useful information! I will keep that workaround in mind and am glad to hear that. Thanks, Coby ...
written 3.1 years ago by Coby Viner50
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Comment: C: ChIPQC without peak data fails to generate a report (due to invocation of plotCo
... Resolved in ChIPQC 1.8.8. ...
written 3.1 years ago by Coby Viner50
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Comment: C: ChIPQC without peak data fails to generate a report (due to invocation of plotCo
... Thanks so much, Tom! ...
written 3.1 years ago by Coby Viner50
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Comment: C: ChIPQCreport yields a cryptic error if "Replicate" data is not specified
... Thanks, Rory! Might it be possible to add a check for that within ChIPQCreport itself (and for it to automatically use the ChIPQCsample object, from the ChIPQCexperiment), to prevent users from needing to use a workaround with only a single sample (i.e. to maintain a consistent API)? ...
written 3.1 years ago by Coby Viner50

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