Daniel Weinberger, PhD

ExcessILI facilitates formatting line list data from syndromic surveillance datasets into time series, and enables analysis of these data to detect increases in reporting above the seasonal baseline. For US data, there is an option to automatically adjust the data for state-specific flu activity (using data from NREVSS and/or state-specific RSV activity (based on Google search volume). The user can either start with line list data, or formatted time series data. An rshiny app is provided to examine data products.

Faculty: Daniel Weinberger, PhD

Download: GitHub / ExcessILI package

Platform: R

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SeroCall can identify and quantitate the capsular serotypes in Illumina whole-genome sequencing samples of S. pneumoniae, calculating abundances of each serotype in mixed cultures. The software is written in Python (compatible with Python 2 or 3), and is freely available under an open source GPLv3 license.

Faculty: James Knight, PhD, Daniel Weinberger, PhD

Download: GitHub / SeroCall package

Platform: Python

Reference: doi.org (SeroCall)

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