Keshif is a web-based tool that lets you browse and understand datasets easily.
Keshif is ready to load your structured data, whether it be digital collections, books that you have read, contact lists, public data sources, movies, etc. It can automatically import data from Google SpreadSheets and CSV/TEXT files. You can write your own importers in Javascript for JSON, XML, even HTML or BibTeX for publication databases.
dc.js is a javascript charting library with native crossfilter support and allowing highly efficient exploration on large multi-dimensional dataset (inspired by crossfilter's demo). It leverages d3 engine to render charts in css friendly svg format. Charts rendered using dc.js are naturally data driven and reactive therefore providing instant feedback on user's interaction. The main objective of this project is to provide an easy yet powerful javascript library which can be utilized to perform data visualization and analysis in browser as well as on mobile device.
Heat*seq is an attempt to make genome-wide comparison of high throughput sequencing experiments easier. It currently works with gene expression data (RNA-seq), with transcription factor ChIP-seq data, and with CAGE data. To get started, select HeatRNAseq, HeatChIPseq or HeatCAGEseq and read the instructions.
Taverna allows you to define how your data flows between the services, without having to worry how you are going to invoke these services. It will automate and pipeline processing of your data.
The Refinery Platform is a web-based data visualization and analysis system powered by an ISA-Tab-compatible data repository for public and private data sets. Analyses are implemented as Galaxy workflows and executed through the Galaxy API.
Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data, and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis' exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection, and an API that supports the batch submission of jobs.
brat is a web-based tool for text annotation; that is, for adding notes to existing text documents.
brat is designed in particular for structured annotation, where the notes are not freeform text but have a fixed form that can be automatically processed and interpreted by a computer.
the following screenshot shows a simple example where a sentence has been annotated to identify mentions of some real-world entities (things) and their types, and a relation between two.
I wonder how ubit2 compares with all the other options out there. Here's a quick list that I hope to continue editing as I survey the field.
Related work
Client-side
Morpheus
Joshua Gould from Broad developed a web tool for exploring matrices of data.
You can load your own data into Morpheus with an API call: https://clue.io/morpheus/linking.html
BrowserGenome
Map reads and count them with javascript in the browser.
QuickRNAseq
Use Nozzle and canvasXpress to visualize pre-computed results from RNA-seq analysis.
RAW
DC.js
Brainscope
https://www.ncbi.nlm.nih.gov/pubmed/28132031
Server-side
Heat*seq
https://github.com/gdevailly/HeatStarSeq_gh
Galaxy
Create workflows and execute them on the server. Lots of tools available: https://toolshed.g2.bx.psu.edu/
Taverna
Create workflows and execute them: http://www.taverna.org.uk/introduction/taverna-features/
GenePattern
Create workflows and execute them. Hosted at Broad.
Babelomics
Launches jobs on a server and shows you the results, very slow.
Refinery
Launches jobs on a server and shows you results.
Oasis
MAGI
http://www.nature.com/nmeth/journal/v12/n6/full/nmeth.3412.html
brat