Leonardo Collado-Torres
Leonardo Collado-Torres
The GTEx and TCGA datasets are some of the most used datasets. With the potential reduced memory usage via #11, it might become feasible to have user guides (vignettes) that...
We want to revise and update the current documentation. In particular, users frequently ask how to best transform the `raw_counts`. We plan to split the current documentation into multiple guides...
We want to write a user guide (vignette) documenting how users can create their own collections (similar to the `recount-brain` one), test them locally, and potentially share them. As part...
`recount3` supports collections, which are samples from multiple studies with extra custom metadata. We want to make `recount-brain` collection (described at https://doi.org/10.1101/618025) available via `recount3`. Doing so will enable us...
Related to #41, we want to upload all the data available at IDIES and also at AWS Open Data Sponsorship Program https://aws.amazon.com/marketplace/pp/prodview-t3rflz3f557jq#resources to AnVIL https://anvilproject.org/. We might have to re-organize...
Assuming that we do complete the data uploads to AnVIL https://anvilproject.org/, we would then update `recount3` to make sure that it is compatible with the data hosted there if you...
As a note to myself, in our meeting with @ChristopherWilks and @Nick-Eagles today, the idea of using a text file like the `homes_index` at https://github.com/LieberInstitute/recount3/blob/master/R/project_homes.R#L44 but for the annotation options...
Right now `spatialLIBD` is built upon the `SpatialExperiment` container class. There is also https://bioconductor.org/packages/SpatialFeatureExperiment/ that can support non-Visium spatially-resolved data. As new technologies come online, we will see which container...
We want to use `rlang` and `cli` to improve the user experience. See https://lcolladotor.github.io/jhustatcomputing2023/posts/18-debugging-r-code/#errors-%C3%A0-la-tidyverse for a quick intro into how these functions improve error messages.
Translate to Spanish the short workshop #68 and other intro level materials to help increase access to these technologies to Spanish-speaking individuals. This will help increase diversity of our user...