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https://github.com/fomightez/millefy-binder
Millefy tool by Ozaki et al. 2020 packaged so it works in launches via MyBinder.org.
https://github.com/fomightez/millefy-binder
Last synced: 6 days ago
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Millefy tool by Ozaki et al. 2020 packaged so it works in launches via MyBinder.org.
- Host: GitHub
- URL: https://github.com/fomightez/millefy-binder
- Owner: fomightez
- Created: 2023-10-24T21:14:49.000Z (about 1 year ago)
- Default Branch: master
- Last Pushed: 2023-11-30T21:01:48.000Z (about 1 year ago)
- Last Synced: 2024-11-07T14:12:52.425Z (about 2 months ago)
- Language: Jupyter Notebook
- Size: 299 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Millefy-binder
*tl;dr:*
Click any '`launch`' badge on this page to run Millefy inside your browser without installing anything.
JupyterLab: [](https://mybinder.org/v2/gh/fomightez/millefy-binder/master?labpath=test_millefy.ipynb)
RStudio: [](https://mybinder.org/v2/gh/fomightez/millefy-binder/master?urlpath=rstudio)
---------------
> Millefy tool by Ozaki et al. 2020 packaged so it works in launches via MyBinder.org!
Millefy is R-based software provides genome browser-like visualization of single-cell RNA sequencing (scRNA-seq) datasets.
See more about it in [the associated publication by Ozaki et al. (2020)](https://pubmed.ncbi.nlm.nih.gov/32122302/) or at [the Millefy Github repo](https://github.com/yuifu/millefy).
[The Millefy Github repo](https://github.com/yuifu/millefy) summarizes it succinctly with:
>"Millefy is a tool for visualizing read coverage of single-cell RNA sequencing (scRNA-seq) datasets in genomic contexts. By dynamically and automatically reorder [*sic*] single cells based on 'locus-specific' pseudotime, Millefy highlights cell-to-cell heterogeneity in read covreage [*sic*] of scRNA-seq data."
[Figure 1 of Ozaki et al. 2020](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6542-z/figures/1) provides an excellent overview of the input data, processing, and typical results.
With sessions launched from here, you can choose to either work with Millefy in JupyterLab or RStudio.
The following two sections describe the basics of each in order to get you started.
Using Millefy in RStudio via MyBinder-served sessions
-----------------------------------------------------
RStudio: [](https://mybinder.org/v2/gh/fomightez/millefy-binder/master?urlpath=rstudio)
Step-by-Step:
To keep this landing page a reasonable length, [the step-by-step directions for using Millefy in RStudio provided via MyBinder.org are here in an associated wiki](https://github.com/fomightez/millefy-binder/wiki/Using-Millefy-in-RStudio-via-MyBinder%E2%80%90served-sessions#using-millefy-in-rstudio-via-mybinder-served-sessions).
Using Millefy in JupyterLab via MyBinder-served sessions
-----------------------------------------------------
JupyterLab: [](https://mybinder.org/v2/gh/fomightez/millefy-binder/master?labpath=test_millefy.ipynb)
Step-by-Step:
1. Click the above badge or [click here](https://mybinder.org/v2/gh/fomightez/millefy-binder/master?labpath=test_millefy.ipynb) to launch a Jupyter session where the [test_millefy.ipynb](https://nbviewer.org/github/yuifu/datascience-notebook-millefy/blob/90f30181e77657566bc2b87c0f70fa5118c4c9fb/examples/test_millefy.ipynb), from [datascience-notebook-millefy](https://github.com/yuifu/datascience-notebook-millefy) will open by default with the R kernel attached upon startup of the session.
1. Run the cells in the 'Example usage of Millefy' notebook by using 'Run' > 'Run All Cells' from the main File menu ribbon across the top. Alternatively, click on each cell and hit Shift-Enter to run one at a time. There is a link at the bottom of that notebook to much of the same content using BAM files as the starting input if that interests you. (That notebook in static form can be viewed [here](https://nbviewer.org/github/fomightez/millefy-binder/blob/master/test_millefy_with_included_bam_files.ipynb).)
1. Once you understand the basics, you can adapt the code to run and analyze your own data. (You may wish to install Millefy on your own machine if you think you find you are exceedng the computational resources provided by MyBinder, which may become an issue if you need to convert BAM files, see below.)
You can exit single-document mode with the toggle in the bottom left corner and then click the 'Folder' icon on the tool strip on the left side of the main panel to open the file browser pane in JupyterLab.
Remember to press the disk icon often to save the current notebook in the session and then save anything useful you make back to your local computer as the session is anonymous and ephemeral. ('`File`' > '`Download`'.) In general, **once the session expires or connection times out, your work is gone**. There is a possible avenue of help when working in JupyterLab and your MyBinder-served session times out with the browser window still open, see 'Getting your notebook after your Binder has stopped'. As the process is rather involved and not something anyone would be familiar with from using '*Vanilla*' Jupyter, it is best you try the steps ahead of actually needing 'the safety net'.
Beyond the technical side, for further understanding of Millefy, I strongly suggest seeing [my coverage of using Millefy MyBinder-served RStudio](https://github.com/fomightez/millefy-binder/wiki/Using-Millefy-in-RStudio-via-MyBinder%E2%80%90served-sessions#using-millefy-in-rstudio-via-mybinder-served-sessions) as I supply my experience with [the Tutorial for Millefy](https://github.com/yuifu/millefy/blob/0f2dde5a4ae8fa321f626410bc62db0255090f91/tutorial/Tutorial.md) and variations on the code for the steps.
Attributions & Millefy resources
---------------------------------
Millefy source publication:
Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets. Ozaki H, Hayashi T, Umeda M, Nikaido I. BMC Genomics. 2020 Mar 3;21(1):177. doi: 10.1186/s12864-020-6542-z. [PMID: 32122302](https://pubmed.ncbi.nlm.nih.gov/32122302/)
[The Millefy Github repo](https://github.com/yuifu/millefy), that the developer [Haruka Ozaki (yuifu on GitHub)](https://github.com/yuifu) provided, has both a [Quick example with an included example dataset](https://github.com/yuifu/millefy/blob/0f2dde5a4ae8fa321f626410bc62db0255090f91/tutorial/Quick_example.md) and a [Tutorial for Millefy](https://github.com/yuifu/millefy/blob/0f2dde5a4ae8fa321f626410bc62db0255090f91/tutorial/Tutorial.md). Those form the basis for the guide to using Millefy in RStudio.
The R kernel-based Jupyter document [test_millefy.ipynb](https://nbviewer.org/github/yuifu/datascience-notebook-millefy/blob/90f30181e77657566bc2b87c0f70fa5118c4c9fb/examples/test_millefy.ipynb), included in launched sessions, comes from [datascience-notebook-millefy](https://github.com/yuifu/datascience-notebook-millefy), which is a Docker image for running Millefy on JupyterLab that the deveoper [Haruka Ozaki (yuifu on GitHub)](https://github.com/yuifu) provided. Presumably that could have been used as a foundation to build this repo since MyBinder can take Dockerfiles; however, that is not the recommended way and because this is R-based I preferred to also have it work with RStudio and so going with the recommended configuring approach seemed easier and should be more robust in the long run. Additionally, the use of Anaconda vs. Docker allows builds of the images to be faster as the repo is updated.
Anaconda's page for the bioconda package for installing Millefy in the Anaconda/conda software management system is [here](https://anaconda.org/bioconda/r-millefy).
***Clarifying Software Attribution: I, Wayne, am not involved in the Millefy software at all. Those attributed above are the developers and distributors of Millefy. See their materials, which are highlighted above in this section. I simply set up this repository to make the software useable with RStudio and JupyterLab in a browser without installation headaches, and I expanded on the developer-provided guides some.***