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fix: skip fourDNData pairs parsing for now
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js2264 committed Jan 22, 2024
1 parent b03e08c commit 4e0d682
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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -3,7 +3,7 @@ FROM bioconductor/bioconductor_docker:${BIOC_VERSION}
COPY . /opt/pkg

# Install book package
RUN Rscript -e 'repos <- BiocManager::repositories() ; remotes::install_local(path = "/opt/pkg/", repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE) ; sessioninfo::session_info(installed.packages()[,"Package"], include_base = TRUE)'
RUN Rscript -e 'repos <- BiocManager::repositories() ; remotes::install_github("lawremi/rtracklayer") ; remotes::install_local(path = "/opt/pkg/", repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE) ; sessioninfo::session_info(installed.packages()[,"Package"], include_base = TRUE)'

## Build/install using same approach than BBS
RUN R CMD INSTALL /opt/pkg
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3 changes: 2 additions & 1 deletion inst/pages/disseminating.qmd
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Expand Up @@ -102,7 +102,8 @@ a large storage footprint.

- `type = 'insulation'` will fetch a `.bigwig` track file precomputed by the 4DN consortium. This track corresponds to the genome-wide insulation score computed by `cooltools` as described in @Crane_2015. To know more about this, read [the excerpt from 4DN data portal](https://data.4dnucleome.org/resources/data-analysis/insulation_compartment_scores#insulation_scores_and_boundaries_page_all). Once fetched from the 4DN data portal, the local file can be imported in `R` using the `import` function, which will generate a `RleList` object.

```{r}
```{r eval = FALSE}
## Not evaluated for now
library(rtracklayer)
fourDNData(experimentSetAccession = '4DNES25ABNZ1', type = 'insulation') |>
import(as = 'Rle')
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2 changes: 2 additions & 0 deletions vignettes/stub.Rmd
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Expand Up @@ -5,6 +5,8 @@ vignette: >
%\VignetteEncoding{UTF-8}
---

# OHCA

```{r, echo=FALSE}
# This is adapted from Aaron Lun's approach in OSCA.* books
link <- BiocStyle::Biocbook(
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