Stephen Turner stephenturner
stephenturner
/ biorxiv-full-text-sentiment.r
Created
September 2, 2024 10:11
biorxiv-full-text-sentiment.r
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| library(tidyverse) | |
| library(rvest) | |
| library(tidytext) | |
| ## Function to get full text given a DOI | |
| get_full_text <- function(doi) { | |
| paste0("https://www.biorxiv.org/content/", doi, ".full") |> | |
| rvest::read_html() |> | |
| rvest::html_nodes("div.section") |> | |
| rvest::html_text() |> |
stephenturner
/ biorxiv-api-httr2.R
Created
August 31, 2024 09:11
R code to query bioRxiv API for publication details
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| library(tidyverse) | |
| library(httr2) | |
| # Set URL path variables | |
| url <- "https://api.biorxiv.org/" | |
| what <- "details" | |
| server <- "biorxiv" | |
| date1 <- "2014-01-01" | |
| date2 <- "2023-12-31" |
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| # Get / clean data ---- | |
| library(tidyverse) | |
| library(httr2) | |
| # Set URL path variables | |
| url <- "https://api.biorxiv.org/" | |
| what <- "details" | |
| server <- "biorxiv" | |
| date1 <- "2014-01-01" | |
| date2 <- "2023-12-31" |
stephenturner
/ vscode-rstudio-keybindings.json
Created
November 18, 2022 18:27
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| // Place your key bindings in this file to overwrite the defaults | |
| [ | |
| // RStudio: Copy lines up/down with alt+cmd+up/down | |
| { | |
| "key": "alt+cmd+down", | |
| "command": "editor.action.copyLinesDownAction", | |
| "when": "editorTextFocus && !editorReadonly" | |
| }, | |
| { | |
| "key": "shift+alt+down", |
stephenturner
/ 1-train-deploy.R
Created
July 26, 2022 10:52
Train and deploy a random forest with vetiver + plumber
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| # R session 1: model training and deployment ------------------------------ | |
| library(tidymodels) | |
| library(vetiver) | |
| library(plumber) | |
| # Not the way you'd actually split data - for demo only | |
| cars_train <- mtcars[1:24,] | |
| cars_test <- mtcars[25:32,] |
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| #!/usr/bin/env python | |
| # Adds allelic depth (AD)=2 to a VCF. | |
| # Usage: bcftools view my.vcf.gz | addad.py | bcftools sort -Oz -o my.ad.vcf.gz && tabix my.ad.vcf.gz | |
| import pysam | |
| vcf_in=pysam.VariantFile("-","r") | |
| vcf_in.header.formats.add("AD",".","Integer","Allelic depth, hard-coded as 2") |
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| # Start window and pane indices at 1 instead of 0 | |
| set -g base-index 1 | |
| set -g pane-base-index 1 | |
| # Shift arrow keys to move around panes | |
| bind -n S-Up select-pane -U | |
| bind -n S-Down select-pane -D | |
| bind -n S-Left select-pane -L | |
| bind -n S-Right select-pane -R |
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| n <- 1e7 | |
| x <- sample(n, size=n, replace=TRUE) | |
| length(unique(x))/n | |
| # [1] 0.6321897 | |
| 1-exp(-1) | |
| # [1] 0.6321206 |
stephenturner
/ build-install-bcftools-home.sh
Last active
November 24, 2021 13:14
Install htslib, bcftools, samtools to home directory
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| # Compile and install htslib, bcftools, samtools 1.9 to home directory | |
| # Set up dirs where stuff will be installed | |
| mkdir -p ${HOME}/bin/htslib | |
| mkdir -p ${HOME}/bin/bcftools | |
| mkdir -p ${HOME}/bin/samtools | |
| # Make a dir to build | |
| mkdir -p ${HOME}/tmp |
stephenturner
/ get-licenses-for-loaded-packages.R
Created
September 26, 2019 15:44
Code to get license information for all loaded packages
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| # Load some packages | |
| library(knitr) | |
| library(tidyverse) | |
| library(DT) | |
| # Get licenses for all installed packages. | |
| installed_licenses <- installed.packages() %>% | |
| as.data.frame() %>% | |
| rownames_to_column("package") %>% | |
| as_tibble() %>% |
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