hackyhourUWA

A running log of things we have managed to fix, and resources we have found along the way!

2022-05-04

Attendants: 9

• Fixed a problem with running rstudio-server via singularity's rocker/rstudio image. Misses libgpng and libgeos. Dave Tang has an image here that contains libpng, but misses libgeos: https://davetang.org/muse/2021/04/24/running-rstudio-server-with-docker/ Philipp made a version that includes libgeos so Seurat can be installed: https://hub.docker.com/repository/docker/philippbayer/rstudio/ (should be philippbayer/rstudio:latest which will install v4.0.5)
• Fixed a barchart to add errorbars and use nicer scaling via scales:label_number()
• discussed Bayesian optimisation for scikit-learn

2022-04-05

Attendants: 8

• Fixed problems with {glmnet} packackage by converting input matrices from character matrices to numeric matrices

  • suggested to move the analysis to tidymodels at some point - support exists https://parsnip.tidymodels.org/reference/glmnet-details.html

• learnt how to test for vectors being in other vectors in julia using in()

  • in.(data.column, [vectors]) to create logical vector to subset data rows
  • important to broadcast the in() function, and also put the vectors in its own array with [] to broadcast against
  • also learned innerjoin(), intersect(), union() to compare and merge two data-frames

• fixing Julia Versions, after installing a new version of julia

• Pkg.add("IJulia"); Pkg.build("IJulia") this will re-register the new kernal which Jupyter notebooks etc and anything that requires the kernal.

• Showed cloudstor.aarnet.edu.au to transfer < 1TB of data internationally (upload via webpage, or use curl https://www.solved.tips/aarnet-cloudstor-using-curl-command-line/ )

• Played around with visualising PC1, PC2, PC3 across RNAseq datasets using ggplot - use facet_wrap(~GROUP) to check how groups look

2022-03-29

Attendants: 7

• turn your for loops into lapply() instead
• Install Rtools for Windows to install {Rcpp} and other packages properly on Windows.
• Wrote a tiny Python script that parses an Ensembl gff3 to pull out functional annotation for mRNAs
• Discussed modeling of turtle movement - showed the usefulness of tidymodels and the upcoming tidymodels book https://www.tmwr.org/
• Showed the Profiler in RStudio for long-running code
• Introduced Julia to people who need to run many computationally-intensive models