cellxgene/ROADMAP.md

cellxgene roadmap

We are very exited for cellxgene to become a valuable tool in collaborations between computational biologists and experimental biologists working on single-cell transcriptomics data. cellxgene is in active development, and we would love to include the community as we plan new features to work on. If you have questions of feedback about this roadmap, please submit an issue on GitHub.

Please note: this roadmap is subject to change.

Last updated: April 11, 2019

what we are building now

In the near term, our goal is to enable teams of computational and experimental biologists to collaboratively explore and annotate their single-cell RNA-seq data.

There are 4 key features we plan to implement in the near term.

• Click install and launch
• Manual annotation workflows
• Toggle embeddings
• Gene information

simple install and launch

The command line interface for installing and launching cellxgene is a barrier for users who are not used to Python or using the command line. We plan to support installation and launch of cellxgene on Mac and Windows. See Issue #687 for more details.

manual annotation workflows

The exploratory visualization that cellxgene offers is critical for manual annotation workflows, especially in collaborative environments. We plan to support manually annotate cells with labels (i.e., cell type or QC flags) for downstream analysis. See Issue #524 for more details.

toggle embeddings

While a single dataset may have multiple embeddings calculated (tSNE, umap, in situ coordinates, trajectories, etc), cellxgene currently requires the user to select the embedding to use in the main layout at launch. We plan to support letting users toggle between any embedding present in a file from the cellxgene interface. See Issue #594 for details.

gene information

Differential expression returns only the names of genes, but no additional information about gene metadata, function, or known associations. We plan to help users learn more about genes they discover by exposing additional gene metadata. See Issue #96 for details.