Martin Morgan mtmorgan
mtmorgan
/ tabula-muris-sensis.R
Last active
December 23, 2022 22:00
Tabula muris liver discovery & visualization
View tabula-muris-sensis.R
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ## | |
| ## 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
View hca2021bioc.R
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ## | |
| ## 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
View hca-demo-sept-7-2021.R
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| options(width=160) | |
| library(dplyr) | |
| ## BiocManager::install("Bioconductor/hca") | |
| library(hca) | |
| ## projects available in the HCA | |
| projects <- projects() | |
| projects | |
| ## a specific project |
View week-2-demo.R
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |
View AWS_ECS_REST.Rmd
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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
View dep-graph.R
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
View deps_broken.R
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
View obo_graph.R
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |
View bioc_first_appearance.R
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(yaml) | |
| library(dplyr) | |
| library(tibble) | |
| library(lubridate) | |
| library(readr) | |
| library(memoise) | |
| get_releases <- | |
| function() | |
| { |
NewerOlder