search

neurogenomics / MAGMA_Celltyping

Find causal cell-types underlying complex trait genetics
https://neurogenomics.github.io/MAGMA_Celltyping
71 stars 31 forks source link

Almost all CTDs are not available #131

Closed AMCalejandro closed 1 year ago

AMCalejandro commented 1 year ago

Hi,

Most of the CTD datasets are actually not available.....

I wonder if this has an easy fix.... It would be so helpful.

ctd_name = c("ctd_AIBS", "ctd_allKI", "ctd_BlueLake2018_FrontalCortexOnly",
    "ctd_BlueLake2018_VisualCortexOnly", "ctd_DivSeq", "ctd_DRONC_human",
    "ctd_DRONC_mouse", "ctd_Saunders", "ctd_Tasic", "ctd_Zeisel2015", "ctd_Zeisel2018",
    "ctd_TabulaMuris", "ctd_Aerts2018", "ctd_Aerts2021", "ctd_Avalos2019",
    "ctd_DescartesHuman", "ctd_DescartesHuman_brain", "ctd_HumanCellLandscape",
    "ctd_Jiang2021", "ctd_Han2022", "ctd_Cao2019", "ctd_Raj2018", "ctd_Raj2018",
    "ctd_Farnsworth2020")

save = lapply(ctd_name, function(x) {
  store = try(MAGMA.Celltyping::get_ctd(x))
})

image

AMCalejandro commented 1 year ago

Added a PR to fix

AMCalejandro commented 1 year ago

Making sure the user has a personal access token makes download to work

image

bschilder commented 1 year ago

This has been a recurrent issue with piggyback: https://github.com/ropensci/piggyback/issues/49

What version of piggyback / R / MAGMA.Celltyping were you using?

In the future, please use the ISSUES template when reporting bugs. This will help developers to better assess and fix the issues.