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seandavi / download_biosample.R
Created Jul 22, 2021
download all of EBI biosample as json
View download_biosample.R
start_date='2000-01-01'
end_date = '2021-12-31'
datefilter = function(date) {
startdate = format(date,'%Y-%m-%d')
return(sprintf("dt:release:from=%suntil=%s",startdate,startdate))
}
download_biosample = function(date) {
require(httr)
View bioc_workshop_template.md

output: rmarkdown::html_document: highlight: pygments toc: true toc_depth: 3 fig_width: 5 bibliography: "r system.file(package='dummychapter1', 'vignettes', 'bibliography.bib')" vignette: > %\VignetteIndexEntry{dummychapter1}

View gist:1a1d1f59d872bf793bcfb3eb4b37fdf3
### Keybase proof
I hereby claim:
* I am seandavi on github.
* I am seandavi (https://keybase.io/seandavi) on keybase.
* I have a public key ASAQ8VtxEXZOXbXUmfgPSsE2L-mF4g5oHcMRkosW0EszDgo
To claim this, I am signing this object:
@seandavi
seandavi / README.ipynb
Last active Sep 21, 2020
sars2pack jupyter notebook for Cornell comp bio talk
View README.ipynb
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@seandavi
seandavi / nextflow_trace_columns.tsv
Created Jul 8, 2020
nextflow_trace_columns.txt
View nextflow_trace_columns.tsv
Name Description
task_id Task ID.
hash Task hash code.
native_id Task ID given by the underlying execution system e.g. POSIX process PID when executed locally, job ID when executed by a grid engine, etc.
process Nextflow process name.
tag User provided identifier associated this task.
name Task name.
status Task status.
exit POSIX process exit status.
module Environment module used to run the task.
@seandavi
seandavi / covid_cases_by_largest_country.R
Created Jun 25, 2020
Countries vying for largest share of new COVID-19 cases
View covid_cases_by_largest_country.R
library(sars2pack)
library(dplyr)
library(zoo)
library(cowplot)
library(ggplot2)
y = ecdc_data() %>% dplyr::group_by(iso3c) %>%
add_incidence_column(count_column = 'confirmed') %>%
align_to_baseline(confirmed>50,group_vars = 'iso3c') %>%
dplyr::arrange(date) %>%
View sars2pack_workflow_gb_2020-06-16.R
browseURL('https://seandavi.github.io/ITR/r_intro_mechanics.html')
1 + 1
x = 10
x
y = 20
y
y + x
browseURL('https://seandavi.github.io/ITR/vectors.html')
# vectors
@seandavi
seandavi / README.md
Last active Jun 12, 2020
Example of using R to build a working web API
View README.md

Example R API

To use, clone this repository and then run:

Rscript api.R

Test using the following URLs:

@seandavi
seandavi / README.md
Last active Jul 8, 2020
Run a Bioconductor Workshop docker image on Google Cloud Platform
View README.md

Run a Bioconductor Workshop on a Google Cloud Instance

To run one of the workshops for Bioc2020, follow these steps after determining which workshop you'd like to run and finding the docker image name. Substitute the docker image name below for tidytranscriptomics if desired.

Prereqs

  • A google cloud platform account (which you can create with $300 free credit if you don't have one)
  • Installed google cloud sdk (the gcloud command)
@seandavi
seandavi / index.Rmd
Created Jun 4, 2020
Bioconductor big data notes
View index.Rmd
---
title: "Big Data Approaches"
subtitle: "Where to go with Bioconductor"
event: "Bioconductor Technical Advisory Board Meeting"
#author: Sean Davis
date: "`r Sys.Date()`"
output:
BiocStyle::html_document
---