DepecheR - Determination of essential phenotypic elements of clusters in high-dimensional entities
The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.
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softwarecellbasedassaystranscriptiondifferentialexpressiondatarepresentationimmunooncologytranscriptomicsclassificationclusteringdimensionreductionfeatureextractionflowcytometryrnaseqsinglecellvisualizationcpp
4.60 score 456 downloadsflowSpecs - Tools for processing of high-dimensional cytometry data
This package is intended to fill the role of conventional cytometry pre-processing software, for spectral decomposition, transformation, visualization and cleanup, and to aid further downstream analyses, such as with DepecheR, by enabling transformation of flowFrames and flowSets to dataframes. Functions for flowCore-compliant automatic 1D-gating/filtering are in the pipe line. The package name has been chosen both as it will deal with spectral cytometry and as it will hopefully give the user a nice pair of spectacles through which to view their data.
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softwarecellbasedassaysdatarepresentationimmunooncologyflowcytometrysinglecellvisualizationnormalizationdataimport
4.56 score 6 stars 9 scripts 524 downloadsislify - Automatic scoring and classification of cell-based assay images
This software is meant to be used for classification of images of cell-based assays for neuronal surface autoantibody detection or similar techniques. It takes imaging files as input and creates a composite score from these, that for example can be used to classify samples as negative or positive for a certain antibody-specificity. The reason for its name is that I during its creation have thought about the individual picture as an archielago where we with different filters control the water level as well as ground characteristica, thereby finding islands of interest.
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softwarecellbasedassaysbiomedicalinformaticsfeatureextractionvisualizationpathwaysclassificationopenjdk
3.30 score 2 scripts 247 downloads