sincell: R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sincell")
AuthorMiguel Julia <migueljuliamolina@gmail.com>, Amalio Telenti <atelenti@jcvi.org>, Antonio Rausell <antonio.rausell@isb-sib.ch>
Bioconductor views BiomedicalInformatics CellBiology Clustering FunctionalGenomics GeneExpression GeneSetEnrichment GraphAndNetwork RNASeq Sequencing SystemsBiology Visualization
Date of publicationNone
MaintainerMiguel Julia <migueljuliamolina@gmail.com>, Antonio Rausell<antonio.rausell@isb-sib.ch>
LicenseGPL (>= 2)
Version1.8.0
http://bioconductor.org/

View on Bioconductor

Man pages

ExpressionMatrix: Single-cell expression data for genes differentially...

f_distance2vector: Conversion of the lower triangular matrix of a distance...

geneset.list: Example of a geneset collection

knnalgorithm: Auxiliary function for KNN and IMC algorithms

pseudoreplicatesbymodel: Auxiliary function of sc_InSilicoCellsReplicatesObj function...

pseudoreplicatesbynoise: Auxiliary function of sc_InSilicoCellsReplicatesObj function...

pseudoreplicatesbynoise_cv2: Auxiliary function of sc_InSilicoCellsReplicatesObj function...

sc_AssociationOfCellsHierarchyWithAGeneSet: Association of a cell-state hierarchy with a functional gene...

sc_clusterObj: Clustering of individual cells based on a metric of choice

sc_ComparissonOfGraphs: Comparisson of graphs

sc_DimensionalityReductionObj: Dimensionality reduction of an expression matrix

sc_distanceObj: Assessment of a cell-to-cell distance matrix with a metric of...

sc_GraphBuilderObj: Graph building function for assessment of cell-state...

sc_InitializingSincellObject: Function to initialize a sincell object

sc_InSilicoCellsReplicatesObj: In silico generation of replicates of individual cells

sc_marker2color: Palette of colors from the expression values of a marker gene

sc_StatisticalSupportByGeneSubsampling: Statistical support of cell-state hierarchies by gene...

sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates: Statistical support of cell-state hierarchies by random cell...

sstalgorithm: Auxiliary function for SST algorithm within function...

Functions

ExpressionMatrix Man page
f_distance2vector Man page
geneset.list Man page
knnalgorithm Man page
pseudoreplicatesbymodel Man page
pseudoreplicatesbynoise Man page
pseudoreplicatesbynoise_cv2 Man page
sc_AssociationOfCellsHierarchyWithAGeneSet Man page
sc_clusterObj Man page
sc_ComparissonOfGraphs Man page
sc_DimensionalityReductionObj Man page
sc_distanceObj Man page
sc_GraphBuilderObj Man page
sc_InitializingSincellObject Man page
sc_InSilicoCellsReplicatesObj Man page
sc_marker2color Man page
sc_StatisticalSupportByGeneSubsampling Man page
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates Man page
sstalgorithm Man page

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