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Merged
ryanstraight merged 1 commit into from
Sep 21, 2026
Merged

Recommend remotes for installing from GitHub #13

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4 changes: 2 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -899,8 +899,8 @@ framework text needs to be staged for this path.
### R

``` r
# install.packages("pak")
pak::pak("ryanstraight/cybedtools")
# install.packages("remotes")
remotes::install_github("ryanstraight/cybedtools")
```

### Python
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4 changes: 2 additions & 2 deletions README.qmd
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Expand Up @@ -553,8 +553,8 @@ Install the package, then fetch the public data release: hash-verified per-frame
### R

```r
# install.packages("pak")
pak::pak("ryanstraight/cybedtools")
# install.packages("remotes")
remotes::install_github("ryanstraight/cybedtools")
```

### Python
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7 changes: 1 addition & 6 deletions concordance/about.qmd
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Expand Up @@ -33,16 +33,11 @@ Every number, table, and lookup widget on this site is derived from the same pac
## Install cybedtools

```r
# Option A: remotes
install.packages("remotes")
remotes::install_github("ryanstraight/cybedtools")

# Option B: pak (faster on first install)
install.packages("pak")
pak::pkg_install("ryanstraight/cybedtools")
```

The package depends on `rdflib`, `jsonlite`, `dplyr`, `purrr`, and `tibble`. See [Start](start/install.qmd) for the full staging pipeline (framework source data, ingestion, graph assembly, query loading).
Python: `pip install cybedtools`. See [Start](start/install.qmd) for fetching the data release and a first query.

## How to cite

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4 changes: 2 additions & 2 deletions concordance/start/install.qmd
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Expand Up @@ -8,8 +8,8 @@ subtitle: "Install the package, fetch the data, run your first query"
### R

```{.r}
install.packages("pak")
pak::pak("ryanstraight/cybedtools")
install.packages("remotes")
remotes::install_github("ryanstraight/cybedtools")
```

### Python
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4 changes: 2 additions & 2 deletions vignettes/getting-started.Rmd
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Expand Up @@ -37,8 +37,8 @@ A single SPARQL query targeting `cybed:RoleElement` returns atomic elements acro
```{r}
#| eval: false
# Install from GitHub (not yet on CRAN)
# install.packages("pak")
pak::pak("ryanstraight/cybedtools")
# install.packages("remotes")
remotes::install_github("ryanstraight/cybedtools")
```

The package depends on `rdflib` for RDF/SPARQL, `jsonlite` for JSON-LD I/O, and a small subset of the tidyverse (`dplyr`, `purrr`, `tibble`). A native Python package with the same API is on PyPI: `pip install cybedtools`.
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