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Phinch is an open-source framework for conducting novel, exploratory analyses of biological datasets, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive and the Bik Lab at UC Riverside. Whether it's genes, proteins, or microbial species, Phinch provides an interactive visualization tool that allows users to explore and manipulate large -Omics datasets.
Phinch 2.0 is a standalone desktop App compatible with Mac OS X, Windows, and Linux operating systems. It currently supports downstream analyses of Biological Observation Matrix (BIOM) files, a standardized file format typically used to represent diverse types of genomic data. The Phinch 2.0 app now supports both BIOM v1.0 (JSON-formatted) and BIOM v2.0 (HDF5-formatted) files, the standard outputs from the QIIME1 and QIIME2 pipelines, respectively. Any type of tab-delimited file containing biological data can be converted into a BIOM file within QIIME itself or using the standalone biom-format python package (see Data Formatting and Loading guide below). All sample metadata and taxonomy/ontology information MUST be embedded in the BIOM file before being loaded into the Phinch App.
- Data Formatting and Loading - quick start guide for formatting your BIOM files and associated sample metadata for use in Phinch 2.0
- Visualization Features - screenshots and tour of Phinch 2.0 visual features
- Tutorials - use case visualization examples using community Flagship Datasets
- Phinch 2.0 Slack Channel - Community Discussion and Troubleshooting
- Phinch 2.0 homepage - Download links for App and Flagship Datasets
- Bug Reports - please report all bugs and software errors on our GitHub issue tracker
- Developer Info and Release Notes
Our draft manuscript is currently available as a preprint on bioRxiv. Please cite Phinch as follows:
Bik, H.M. and Pitch Interactive (2014) Phinch: An interactive, exploratory data visualization framework for –Omic datasets, bioRxiv, doi: http://dx.doi.org/10.1101/009944
The Phinch 2.0 Desktop app is compatible with Mac OS X, Windows, and Linux operating systems. Separate downloads for each of these operating systems are available on the Phinch 2.0 homepage