Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fixed links on paragraphs 24 & 26 #265

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Fixed links on paragraphs 24 & 26 #265

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,15 +15,15 @@ Functions for running and comparing many different clusterings of single-cell se

Risso D, Purvis L, Fletcher R, Das D, Ngai J, Dudoit S, Purdom E (2018) "clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets" PLoS Comput Biol. 2018 Sep 4;14(9):e1006378 [link](http://dx.plos.org/10.1371/journal.pcbi.1006378)

There is a github repository ([epurdom/RSECPaper](https://github.com/epurdom/RSECPaper) for this paper that gives the code for reproducing the analysis in that manuscript.
There is a github repository ([epurdom/RSECPaper](https://github.com/epurdom/RSECPaper)) for this paper that gives the code for reproducing the analysis in that manuscript.

* A [F1000 workflow](https://f1000research.com/articles/6-1158/v1) demonstrating the use of RSEC for clustering as part of trajectory estimation with the package `slingshot` and normalization with `zinbwave`

Perraudeau F, Risso D, Street K, Purdom E, and Dudoit S (2017) "Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference" F1000Research 6:1158.

* A compiled version of the vignette (i.e. tutorial) of the github version of `clusterExperiment` (corresponding to the `master` branch) can be found (here)[http://bioconductor.org/packages/devel/bioc/vignettes/clusterExperiment/inst/doc/clusterExperimentTutorial.html]
* A compiled version of the vignette (i.e. tutorial) of the github version of `clusterExperiment` (corresponding to the `master` branch) can be found [here](http://bioconductor.org/packages/devel/bioc/vignettes/clusterExperiment/inst/doc/clusterExperimentTutorial.html)

* The compiled version of the vignette corresponding to the version of `clusterExperiment` available with the latest release of Bioconductor can be found (here)[http://bioconductor.org/packages/release/bioc/vignettes/clusterExperiment/inst/doc/clusterExperimentTutorial.html]
* The compiled version of the vignette corresponding to the version of `clusterExperiment` available with the latest release of Bioconductor can be found [here](http://bioconductor.org/packages/release/bioc/vignettes/clusterExperiment/inst/doc/clusterExperimentTutorial.html)

## Installation instructions

Expand All @@ -37,7 +37,7 @@ if (!requireNamespace("BiocManager", quietly=TRUE))
BiocManager::install("clusterExperiment")
```

To install the most recent version of the package available on the development branch of bioconductor, follow the above instructions, after downloading the development version of bioconductor (see [here](https://www.bioconductor.org/developers/how-to/useDevel/) for instructions).
To install the most recent version of the package available on the development branch of bioconductor, follow the above instructions, after downloading the development version of bioconductor (see [here](https://www.bioconductor.org/developers/how-to/useDevel/) for instructions).

If you are having problems installing/updating the package `gsl` from source because your gsl installation is not found, [this answer](https://stackoverflow.com/a/26616008) (and the comment following it) on stackoverflow may be of help.

Expand Down