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.

Author
Miguel Julia <migueljuliamolina@gmail.com>, Amalio Telenti <atelenti@jcvi.org>, Antonio Rausell <antonio.rausell@isb-sib.ch>
Date of publication
None
Maintainer
Miguel Julia <migueljuliamolina@gmail.com>, Antonio Rausell<antonio.rausell@isb-sib.ch>
License
GPL (>= 2)
Version
1.6.0
URLs

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...

Files in this package

sincell/DESCRIPTION
sincell/NAMESPACE
sincell/NEWS
sincell/R
sincell/R/RcppExports.R
sincell/R/sincell.R
sincell/build
sincell/build/vignette.rds
sincell/data
sincell/data/ExpressionMatrix.rda
sincell/data/datalist
sincell/data/geneset.list.rda
sincell/inst
sincell/inst/CITATION
sincell/inst/doc
sincell/inst/doc/sincell-vignette.R
sincell/inst/doc/sincell-vignette.Rnw
sincell/inst/doc/sincell-vignette.pdf
sincell/man
sincell/man/ExpressionMatrix.Rd
sincell/man/f_distance2vector.Rd
sincell/man/geneset.list.Rd
sincell/man/knnalgorithm.Rd
sincell/man/pseudoreplicatesbymodel.Rd
sincell/man/pseudoreplicatesbynoise.Rd
sincell/man/pseudoreplicatesbynoise_cv2.Rd
sincell/man/sc_AssociationOfCellsHierarchyWithAGeneSet.Rd
sincell/man/sc_ComparissonOfGraphs.Rd
sincell/man/sc_DimensionalityReductionObj.Rd
sincell/man/sc_GraphBuilderObj.Rd
sincell/man/sc_InSilicoCellsReplicatesObj.Rd
sincell/man/sc_InitializingSincellObject.Rd
sincell/man/sc_StatisticalSupportByGeneSubsampling.Rd
sincell/man/sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates.Rd
sincell/man/sc_clusterObj.Rd
sincell/man/sc_distanceObj.Rd
sincell/man/sc_marker2color.Rd
sincell/man/sstalgorithm.Rd
sincell/src
sincell/src/RcppExports.cpp
sincell/src/pseudoreplicatesbymodel.cpp
sincell/src/pseudoreplicatesbynoise.cpp
sincell/src/pseudoreplicatesbynoise_cv2.cpp
sincell/src/sstalgorithm.cpp
sincell/vignettes
sincell/vignettes/sincell-vignette.Rnw