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Create a directory and Rmd that uses the output of #5 as the input. Then show how to explore the data (PCA), check the ERCCs (Nick can do this part), normalize the data, perform a differential express…
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Hi,
While writing #66 and in particular, while checking https://github.com/LieberInstitute/SPEAQeasy/blob/master/scripts/build_annotation_objects.R#L125 I noticed that some R commands are written i…
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Similar to #1, at https://github.com/LieberInstitute/VisiumImgProcessing/blob/705329a25b21f818e62a3606fec4a7af1f757192/Step1.Rmd#L3 or maybe before, I would add a code chunk or description telling rea…
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We'll want to host the output files from SPEAQeasy from this example, such that others can run the downstream analyses and that we can then point users to the output files in the SPEAQeasy docs. Depen…
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Add a directory and a Rmd or R file with the code for selecting around 40 RNA-seq samples from one of the public LIBD projects (BrainSeq Phase I, II or maybe even III; stem cell; DG; BPD, ...) with:
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Most notably, information about docker setup is scattered throughout the README, often redundant, and the container versions are outdated. Other adjustments will be made in response to new users of th…
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## Bug report
On a server with 144 cores, when resuming a bioinformatics workflow processing 800 samples with multiple processes/stages, the local executor runs hits the upper limit of the thread po…
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Copy and adapt https://github.com/leekgroup/recount-analyses/blob/gh-pages/index.Rmd to this repo. Include the `.nojekyll` file. The rendered `index.html` file will become the homepage for this repo (…
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In the README and manuscript, we claim that one can copy a main script (e.g. `run_pipeline_sge.sh`), modify the path to nextflow in the copied script, and now SPEAQeasy can be shared by another user i…
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Use ~ 24 samples from BrainSeq Phase 2 with about 5 of them with issues
Select same subjects DLPFC and HIPPO
+ a few mismatched
+ a few low quality