To unlock to the iSEE bioconductor package for transcript-level visualization in the context single-cell omics experiments. The idea is to have additional panels to supplement the established (gene-level) visualizations of iSEE with relevant transcript-level plots. An end-user should be able to select a gene or transcript of interest and to readily obtain relevant information at the level of the individual isoforms.
Visualizing the raw usage of transcript, i.e. by generating a violin plot on the fraction of the expression of a target transcript and the expression of its corresponding gene:
Adopting/adapting the DTU visualization provided by DRIMSeq:
Visualizing gene models as provided in ggbio. Note that this requires interaction with GRanges, which has not been implemented in iSEE yet.
altExp
or MultiAssayExperiment
to facilitate the visualization of multimodal data with iSEE.This project should obviously be compatible with existing bioconductor concepts, including established data types and workflows. Therefore, we suggest the following workflow during the early stages of project;
Link to pkgdown website: https://jgilis.github.io/iSEEtranscripts/
In order to make this a collaborative effort, we suggest forking the original iSEEtranscripts repository, working on a branch of your fork, and submitting a pull request when your contribution is ready for review. In addition, we will use the bioc slack channel eurobioc2020-isee-transcripts for further communication and brainstorming.
This project is created in light of the BiocChallenges project introduced at eurobioc2020.