ImpulseDE statistics

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ImpulseDE specifications

Information


Unique identifier OMICS_13282
Name ImpulseDE
Software type Package/Module
Interface Command line interface
Restrictions to use None
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.
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.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.6.0
Stability Stable
Requirements
stats, parallel, graphics, utils, grDevices, amap, knitr, boot, R(>=3.2.3), compiler, longitudinal
Maintained Yes

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  • person_outline Nir Yosef <>

Publication for ImpulseDE

ImpulseDE in publication

PMCID: 5575496
PMID: 28524227
DOI: 10.1002/1873-3468.12684

[…] can be identified, along with a parameter letting you learn when the switch happens . similarly, an assumption can be that genes be described as a transient pulse over the pseudotime. the package impulsede identifies such genes, while providing parameters for when in pseudotime the pulse occurs ., one important application of scrna‐seq studies is the identification of coregulated modules […]


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ImpulseDE institution(s)
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
ImpulseDE funding source(s)
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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