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# source: Matt Dray's blog: https://www.rostrum.blog/posts/2021-10-05-gorilla/

library(magick)

# download and read the image
img_file <- tempfile(fileext = ".jpg")
download.file(
  paste0(
    "https://classroomclipart.com/images/gallery/",
    "Clipart/Black_and_White_Clipart/Animals/",

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Installation on Mac OS X

brew install datalad wget

Creating a new dataset

First, we create a new, empty dataset. (Reminder: a dataset refers to a folder of files, not any single file.)

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Statistical tests, P values, confidence intervals, and power: a guide to misinterpretations

Excerpted from Greenland et al, Statistical tests, P values, confidence intervals, and power: a guide to misinterpretations, 2016

What P values, confidence intervals, and power calculations don't tell us

Common misinterpretations of single P values

1. The P value is the probability that the test hypothesis is true; for example, if a test of the null hypothesis gave P = 0.01, the null hypothesis has only a 1 % chance of being true; if instead it gave P = 0.40, the null hypothesis has a 40 % chance of being true.

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brew install duckdb

duckdb -c "INSTALL httpfs"

REMOTE_FILE="https://raw.githubusercontent.com/mwaskom/seaborn-data/master/penguins.csv"

# read a remote CSV file in to a duckdb database into an in-memory database
duckdb -c "SELECT * FROM '${REMOTE_FILE}';" 

# By default, the CLI will open a temporary in-memory database. 

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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}