Martin Morgan mtmorgan
mtmorgan
/ tabula-muris-sensis.R
Last active
December 23, 2022 22:00
Tabula muris liver discovery & visualization
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| ## | |
| ## setup | |
| ## | |
| if (!"BiocManager" %in% rownames(installed.packages())) | |
| install.packages("BiocManager", repository = "https://cran.r-project.org") | |
| BiocManager::install( | |
| ## only reinstall if newer version available | |
| c("cellxgenedp", "plotly") | |
| ) |
mtmorgan
/ hca2021bioc.R
Last active
October 6, 2021 12:25
Script used during Human Cell Atlas presentation, 2021-10-06
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| ## | |
| ## Preliminiaries: install infrasctructure and required packages | |
| ## | |
| ## We've got to be using a least R version 4.1 | |
| my_R_version <- | |
| numeric_version(paste(R.Version()[c("major", "minor")], collapse = ".")) | |
| stopifnot(my_R_version >= "4.1") | |
mtmorgan
/ hca-demo-sept-7-2021.R
Created
September 7, 2021 23:09
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| options(width=160) | |
| library(dplyr) | |
| ## BiocManager::install("Bioconductor/hca") | |
| library(hca) | |
| ## projects available in the HCA | |
| projects <- projects() | |
| projects | |
| ## a specific project |
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| if (!"AnVIL" %in% rownames(installed.packages())) | |
| BiocManager::install("AnVIL") | |
| library(AnVIL) | |
| this_workspace = avworkspace() | |
| hca = "featured-workspaces-hca/HCA_Optimus_Pipeline" | |
| thousand_genomes = "anvil-datastorage/1000G-high-coverage-2019" | |
| ## AnVIL 'namespace' / 'name' == workspace |
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| # AWS ECS access via REST | |
| Resources | |
| - [Getting Started with ECS][ECS] | |
| - [REST API][API] | |
| [ECS]: https://docs.aws.amazon.com/AmazonECS/latest/developerguide/getting-started-ecs-ec2.html | |
| [API]: https://docs.aws.amazon.com/AmazonECS/latest/APIReference/Welcome.html |
mtmorgan
/ dep-graph.R
Created
August 14, 2020 16:24
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| package_dependencies <- tools::package_dependencies | |
| trim <- function(deps, drop) { | |
| lvls = names(deps) | |
| df = data.frame( | |
| pkg = factor(rep(names(deps), lengths(deps)), levels = lvls), | |
| dep = unlist(deps, use.names = FALSE) | |
| ) | |
| df = df[!df$dep %in% drop,, drop = FALSE] | |
| split(df$dep, df$pkg) |
mtmorgan
/ deps_broken.R
Created
June 9, 2020 07:18
Query Bioconductor build report for package dependencies that fail to install, build, or check
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| library(BiocPkgTools) | |
| library(dplyr) | |
| deps_broken <- | |
| function( | |
| pkg, | |
| repos = BiocManager::repositories(), | |
| version = BiocManager::version() | |
| ) | |
| { |
mtmorgan
/ obo_graph.R
Last active
April 12, 2020 16:20
construct distance between GO nodes from OBO file
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| obo = readLines("go.obo") | |
| ## | |
| ## Clean data | |
| ## | |
| ## blank lines separate different 'groups' in the obo | |
| group <- cumsum(!nzchar(obo)) | |
| ## keep groups that have the [Term] label |
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| library(yaml) | |
| library(dplyr) | |
| library(tibble) | |
| library(lubridate) | |
| library(readr) | |
| library(memoise) | |
| get_releases <- | |
| function() | |
| { |
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