Contributed analyses

May 11, 2021 · View on GitHub

Contributions

Hackathon	Participant(s)	Title
scNMTseq	Al J Abadi	Multi-block PLS
scNMTseq	Wancen Mu and Michael Love	CV-MOFA
scNMTseq	Josh Welch	LIGER analysis of scNMT-seq
scNMTseq	Arshi Arora	MOSAIC analysis of scNMT-seq
scProteomics	Lauren Hsu	Exploratory analyses
scProteomics	Chen Meng	Predicting partially overlapping data
scProteomics	Pratheepa Jeganathan	Latent Dirichlet Allocation
scProteomics	Yingxin Lin	Integrative analysis of breast cancer survival based on spatial features
scSpatial	Alexis Coullomb	Neighbours Aggregtion
scSpatial	Joshua Sodicoff	Utilizing LIGER for the integration of spatial transcriptomic data
scSpatial	Dario Righelli	SpatialExperiment Analysis
scSpatial	Amrit Singh	seqFISH+scRNASeq integration using semi-supervised glmnet
scSpatial	Hang Xu	Cortex seq-FISH + scRNA data - gene selection
scSpatial	Yuzhou Feng	sPLS-DA and MINT models for cell type prediction and gene selection

How to deploy your own html and containerized report using GitHub Actions

:zero: Choose a name for your package. Recommended convention: {hackathon_event}.{theme}.{method/topic}. e.g. BIRSBIO2020.scNMTseq.Benchmarking, BIRSBIO2020.scProteomics.LatentDirichlet. Ensure that you also have a Docker account for automatic containerization as well.

:one: Use https://github.com/seandavi/BuildABiocWorkshop2020 as template for your analysis package. You can simply click here to accomplish this. Make it public and include all branches (to keep master & gh-pages, you can delete the rest).

:exclamation: For python notebooks also see https://github.com/fastai/fastpages

:two: Follow the steps outlined here to set up your own workflow and create a package from your analyses. The notebooks should go in ./vignettes folder and source files in ./R (or simply include them in notebooks). Include all dependencies in DESCRIPTION and ensure it can be installed, Ensure devtools::build_vignettes() can successfully create the vignettes locally before testing using GitHub Actions.

:bulb: If you use R and have python dependencies, this setup should help as an example.

:bulb: The docker image name should only include lowercase letters, integers, _ and -.

:bulb: Follow this article to add Docker credentials to GitHub Secrets.

:three: Push and ensure the workflow deploys successfully using GitHub Actions (https://github.com/YOUR_GITHUB_USER/REPO/actions)

:four: Add the relevant links and details to the table above through a pull request

:five: Please update these steps through a PR if required