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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
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Building plots with abberant splicing results #495

Open SergeyBioinformatics opened 11 months ago

SergeyBioinformatics commented 11 months ago

Hello. I have an issue with the visualisation of DROP abberant splicing results. The pipeline worked completely and created the result table and html, but in fds, apparently, there is not enough data to visualize graphs for samples and genes. At the time html document has some example plots. Here are screenshots of a problem. assays exprected_observed plot_expressionError Splicing Volcano error

vyepez88 commented 11 months ago

Hi Sergey, at some point we removed the zscores from the fds assays. It could be that you're using an old FRASER version. Please install the latest one (1.99.0) from our github: https://github.com/gagneurlab/fraser

SergeyBioinformatics commented 11 months ago

Thank you for a response! I've checked my Fraser version and it is old (‘1.12.1’). I've tried to update it with if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages('BiocManager') BiocManager::install('FRASER') but got lots of warning messages and several error. Here are mistakes:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace 'htmltools' 0.5.5 is being loaded, but >= 0.5.7 is required Calls: ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace Execution halted ERROR: lazy loading failed for package 'bslib' Error: package 'DelayedArray' 0.26.6 was found, but >= 0.26.7 is required by 'DelayedMatrixStats' Execution halted ERROR: lazy loading failed for package 'DelayedMatrixStats'

I also attach an installation log to this comment. My OS is Windows 10 and I have R 4.3.1 Thank you very much for your help!

fraser_installation_log.txt

SergeyBioinformatics commented 11 months ago

I also unsuccessfully tried to install Fraser with the same command on Ubuntu web server. Here is a log [Uploading ubuntu_installation_log.txt…]()

drewjbeh commented 8 months ago

Hi there, Seems like you're having some issues updating dependencies while upgrading DROP. Perhaps reinstalling a brand new environment would save a lot of time and effort here. Try starting again with a new environment. Or you could see #509 and try the solution mentioned there by installing using the yml file. This is also detailed in the README.

AtaJadidAhari commented 3 weeks ago

Hi @SergeyBioinformatics, any updates on this? Did you try updating FRASER to the newest (currently v1.99.4) version?