User: jared.andrews07

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Posts by jared.andrews07

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Comment: C: DiffBind Heatmap Omitting Results?
... Ah, that clarifies things exceptionally well. Thanks! ...
written 8 months ago by jared.andrews070
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DiffBind Heatmap Omitting Results?
... I'm running into a curious issue with DiffBind's plotHeatmap function when used with a single contrast. It appears to either be omitting some of the results or I'm misusing it. Either way, I'd like to determine the issue. I've run my analysis and identified ~13000 differentially bound sites: > k ...
diffbind heatmap.3 written 8 months ago by jared.andrews070 • updated 8 months ago by Rory Stark2.5k
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Multi-factor blocking in DiffBind
... I was wondering if it's possible to account for multiple factors when analyzing samples in DiffBind. I want to block for potential batch effects as well as treatment conditions, but I'm unsure how to do so (or if it's even possible). The docs make it clear how to block for one factor, but don't make ...
diffbind multiple factor design differential binding analysis written 10 months ago by jared.andrews070 • updated 10 months ago by Rory Stark2.5k
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Answer: A: Unhelpful Errors Running ChIPQC on Computing Cluster
... Yeah, I'm not sure what the issue was here. I managed to get it running locally, so I'm just going to chalk it up to issues with R on the cluster. It does not like running in parallel though, I always have to run it in serial to get it running. Thanks for checking up on it. ...
written 11 months ago by jared.andrews070
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Comment: C: Unhelpful Errors Running ChIPQC on Computing Cluster
... Excellent, thank you. `ChIPQCsample` works just fine on my individual samples, so I don't think there's anything wrong with any of my bam or peak files. I may just go ahead and create the sample objects for each of my samples and try running it with a list of those, inconvenient as it is. Also, it t ...
written 12 months ago by jared.andrews070
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Unhelpful Errors Running ChIPQC on Computing Cluster
... I'm having issues running ChIPQC on a computing cluster, and the errors being thrown aren't particularly helpful. The code: library(ChIPQC) my_experiment = ChIPQC(experiment="CellLine_Experiment_Sheet.csv", annotation="hg19") ChIPQCreport(my_experiment, facetBy=c("Tissue", "Treatment")) warnings ...
chipqc chipqcreport written 12 months ago by jared.andrews070

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