- Unique identifier:
- Command line interface
- Input data:
- An expression table with genes in rows and samples in columns; An annotation table with two columns, one carrying the timestamps as numeric numbers and the other one carrying the condition information.
- Operating system:
- Unix/Linux, Mac OS, Windows
- GNU General Public License version 3.0
- graphics, grDevices, stats, utils, parallel, compiler
- Software type:
- Restrictions to use:
- Output data:
- Fitted impulse model parameters, sum of squared fitting errors as well as the calculated impulse values for all time points; genes differentially expressed according to a specified cutoff together with the adjusted p-values; the adjusted p-values, flags and results of additional tests for all genes; clusters, to which the genes were assigned to, the mean expression values for the clusters.
- Programming languages:
- Computer skills:
- Nir Yosef <>
No open topic.
ImpulseDE: detection of differentially expressed genes in time series data using impulse models.
PMID: 27797772 DOI: 10.1093/bioinformatics/btw665
Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany; Electrical Engineering and Computer Science, Center for Computational Biology, University of California Berkeley, CA, USA
This work was supported by grants U01 MH105979 and U01 HG007910 from the National Institute of Health and partially by SFB704.
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