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---
title: "Controlled vocabulary for sequencing experiments"
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

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---
title: "Experimenting with SQLite"
editor_options: 
  chunk_output_type: inline
---

```{r}
library(glue)
library(RSQLite)
library(jsonlite)

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library(AnnotationDbi)
library(org.Hs.eg.db)
library(GO.db)

kTerm <- "GO:0007265"
# retrieve all genes annotated with the GO germ
df <- AnnotationDbi::select(org.Hs.eg.db, keys  = c(kTerm),
                            columns = c("ENTREZID", "ENSEMBL"), 
                            keytype = "GO")
nrow(df)  # 117 (some duplicate EntrezIds because we requested Ensembl ids, too)

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---
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(crosstalk)
library(gsisdecoder)  # for nflfastR::build_nflfastR_pbp
library(htmltools)
library(nflfastR)

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---
title: "DT, plotly and crosstalk"
---

```{r}
library(plotly)
library(DT)
library(crosstalk)
library(htmltools)
```

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---
title: "Presenting gene set enrichment results with reactable and plotly"
format: 
  html:
    page-layout: full
    code-fold: true
    code-summary: "Show the code"
---

```{r}

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#!/usr/bin/env bash

# This script reads filenames from the FILENAMES text file, prepends each with the URL
# and then uses wget to download them one by one.

set -x  # print the commands as they are executed
set -e  # exit on error
set -o nounset  # no unset variables
set -o pipefail  # if a step in a pipe fails, the whole pipe fails immediately

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#' Retrieve temporary AWS authentication key, secret key and token
#' 
#' Saturn Cloud instances use web authentication to obtain temporary 
#' access to AWS resources, e.g. S3 buckets, instead of environmental variables.
#' But there are situations where the typical `AWS_ACCESS_KEY_ID`,
#' `AWS_SECRET_ACCESS_KEY` and `AWS_SESSION_TOKEN` environmental variables are
#' needed, e.g. to authenticate with tools that don't support web
#' authentication such as the `aws.s3` and `paws` R packages. This function
#' retrieves the temporary variables (but does not export them as environmental
#' variables). 

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library(glue)
library(purrr)
library(rentrez)
library(snakecase)
library(tidyr)
library(xml2)

rentrez::entrez_dbs()  # for reference: available databases

# query NCBI GEO for information about Series GSE178265

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library(vcd)
library(patchwork)

set.seed(123)

# we make 4 independent draws from a poisson
# distribution, fit the poisson distribution
# and then draw the rootogram to compare observed
# and fitted values.
plots <- lapply(1:4, function(draw) {