WaveCrest pipeline

WaveCrest specifications

Information


Unique identifier OMICS_18542
Name WaveCrest
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Some expression matrix, with genes in rows and cells as columns.
Input format CSV
Output data Some normalized expression matrix with genes in row and cells in column following original cell order, cells following recovered order and y-axis shows normalized expression, genes (non-marker) are listed with their corresponding mean squared errors (MSEs).
Output format CSV, PDF, TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Apache License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Li-Fang Chu <>
  • person_outline James Thomson <>

Publication for WaveCrest

WaveCrest IN pipelines

 (2)
2017
PMCID: 5746276
PMID: 29240790
DOI: 10.1371/journal.pbio.2004050

[…] gene clusters. the cyclic orderings were used to identify additional genes following the same orders by fitting a third-degree polynomial to all genes using the wavecrestiden function from the wavecrest [66] r package version 0.0.1. genes were ranked by their fit using the mean squared error (mse), and only the top 100 genes were considered further. the wavecrestiden function was run […]

2017
PMCID: 5746276
PMID: 29240790
DOI: 10.1371/journal.pbio.2004050

[…] mean squared error (mse), and only the top 100 genes were considered further. the wavecrestiden function was run twice, either including zeros in the polynomial fit or treating them as missing. the wavecrest algorithm was also used as above to obtain a cyclic order on the set of unstressed single cells based on five rp genes (s5 table)., length-normalized read counts were taken […]

WaveCrest institution(s)
Morgridge Institute for Research, Madison, WI, USA; Department of Cell & Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, CA, USA; Department of Statistics, University of Wisconsin, Madison, WI, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA; Present address: Genentech, Inc., South San Francisco, CA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
WaveCrest funding source(s)
Supported by the National Institutes of Health 4UH3TR000506-03, 5U01HL099773-06, GM102756, U54 AI117924 and the Charlotte Geyer Foundation, and the Morgridge Institute for Research.

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