diff --git a/website/src/pages/features.md b/website/src/pages/features.md index 41b355caa9..c3ab6336a8 100644 --- a/website/src/pages/features.md +++ b/website/src/pages/features.md @@ -36,20 +36,23 @@ view types ## Feature comparison of JBrowse 2 vs JBrowse 1 -| Feature | JBrowse 2 | JBrowse 1 | -| ------------------------------------------------------------------- | ----------------------- | --------- | -| Status updates during track loading (e.g. Downloading BAM index...) | :heavy_check_mark: | :x: | -| Uses webworkers for parsing and rendering tracks | :heavy_check_mark: | :x: | -| Supports interactive editing of configuration in the app | :heavy_check_mark: | :x: | -| Can "flip" or reverse complement the linear view | :heavy_check_mark: | :x: | -| Hi-C data rendering | :heavy_check_mark: | :x: | -| Can display multiple chromosomes in a single view | :heavy_check_mark: | :x: | -| Sort read pileup in alignments tracks | :heavy_check_mark: | :x: | -| Show soft clipping in alignments tracks | :heavy_check_mark: | :x: | -| Built-in spreadsheet-like view for datasets | :heavy_check_mark: | :x: | -| Can connect to UCSC track hubs | :heavy_check_mark: [^1] | :x: | -| Can load plugins at run-time instead of build time | :heavy_check_mark: [^2] | :x: | -| Non-admin users can open tracks and share them with others | :heavy_check_mark: [^3] | :x: | +| Feature | JBrowse 2 | JBrowse 1 | +| ------------------------------------------------------------------- | ----------------------- | ------------------ | +| Status updates during track loading (e.g. Downloading BAM index...) | :heavy_check_mark: | :x: | +| Uses webworkers for parsing and rendering tracks | :heavy_check_mark: | :x: | +| Supports interactive editing of configuration in the app | :heavy_check_mark: | :x: | +| Can "flip" or reverse complement the linear view | :heavy_check_mark: | :x: | +| Hi-C data rendering | :heavy_check_mark: | :x: | +| Can display multiple chromosomes in a single view | :heavy_check_mark: | :x: | +| Sort read pileup in alignments tracks | :heavy_check_mark: | :x: | +| Show soft clipping in alignments tracks | :heavy_check_mark: | :x: | +| Built-in spreadsheet-like view for datasets | :heavy_check_mark: | :x: | +| Can connect to UCSC track hubs | :heavy_check_mark: [^1] | :x: | +| Can load plugins at run-time instead of build time | :heavy_check_mark: [^2] | :x: | +| Non-admin users can open tracks and share them with others | :heavy_check_mark: [^3] | :x: | +| Re-usable NPM package | :heavy_check_mark: [^3] | :x: | +| Name searching e.g. ability to type a gene name/ID to search for it | :x: | :heavy_check_mark: | +| URL query params API e.g. specifying ?loc=chr1:1-100 in URL bar | :x: | :heavy_check_mark: | [^1] Requires that the trackhub host support CORS for the jbrowse-web, jbrowse-desktop does not require this however @@ -74,3 +77,20 @@ Here is a short list of current data format support - Indexed FASTA/BGZip indexed FASTA - 2bit - .hic (Hi-C contact matrix visualization) + +## Embeddability + +JBrowse 1 has some notion of being embeddable but it is not ideal and it +doesn't have very optimal routes for being packaged and re-used on NPM + +With JBrowse 2 we have some new concepts for embeddability. For example, we can +install just the linear-genome-view and use it as a react component. + +The @jbrowse/react-linear-genome-view is specialized for certain use cases and +is not hooked up to session sharing, URL params, or anything but instead is a +simple React component + +See here for more details https://www.npmjs.com/package/@jbrowse/react-linear-genome-view + +Note that the entire jbrowse-web app that contains multiple views can't +currently be installed via NPM though