Package: speckle 1.5.0

Belinda Phipson

speckle: Statistical methods for analysing single cell RNA-seq data

The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains functions to analyse differences in cell type proportions. There are also functions to estimate the parameters of the Beta distribution based on a given counts matrix, and a function to normalise a counts matrix to the median library size. There are plotting functions to visualise cell type proportions and the mean-variance relationship in cell type proportions and counts. As our research into specialised analyses of single cell data continues we anticipate that the package will be updated with new functions.

Authors:Belinda Phipson [aut, cre]

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NEWS

# Install 'speckle' in R:

install.packages('speckle', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

pbmc_props - Cell type proportions from single cell PBMC data

On BioConductor:speckle-1.5.0(bioc 3.20)speckle-1.4.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

13 exports 0.49 score 165 dependencies

Last updated 2 months agofrom:dd5fa17e91

Exports:convertDataToList estimateBetaParam estimateBetaParamsFromCounts getTransformedProps ggplotColors normCounts plotCellTypeMeanVar plotCellTypeProps plotCellTypePropsMeanVar propeller propeller.anova propeller.ttest speckle_example_data

Dependencies:abind askpass base64enc BH Biobase BiocGenerics bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DelayedArray deldir digest dotCall64 dplyr dqrng edgeR evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leiden lifecycle limma listenv lmtest locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme openssl parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S4Arrays S4Vectors sass scales scattermore sctransform Seurat SeuratObject shiny SingleCellExperiment sitmo sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.utils statmod stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex UCSC.utils utf8 uwot vctrs viridisLite withr xfun xtable XVector yaml zlibbioc zoo

speckle: statistical methods for analysing single cell RNA-seq data

Belinda Phipson

Rendered fromspeckle.Rmdusingknitr::rmarkdownon Jun 25 2024.

Last update: 2022-12-06
Started: 2022-08-19

Help page	Topics
Extract metadata from 'SingleCellExperiment' object	.extractSCE
Extract metadata from 'Seurat' object	.extractSeurat
Convert counts or proportions matrix to list object for propeller	convertDataToList
Estimate the parameters of a Beta distribution	estimateBetaParam
Estimate parameters of a Beta distribution from counts	estimateBetaParamsFromCounts
Calculates and transforms cell type proportions	getTransformedProps
Output a vector of colours based on the ggplot colour scheme	ggplotColors
Normalise a counts matrix to the median library size	normCounts
Cell type proportions from single cell PBMC data	pbmc_props
Plot cell type counts means versus variances	plotCellTypeMeanVar
Plot cell type proportions for each sample	plotCellTypeProps
Plot cell type proportions versus variances	plotCellTypePropsMeanVar
Finding statistically significant differences in cell type proportions	propeller
Performs F-tests for transformed cell type proportions	propeller.anova
Performs t-tests of transformed cell type proportions	propeller.ttest
Generate example data	speckle_example_data

Package: speckle 1.5.0

speckle: Statistical methods for analysing single cell RNA-seq data

speckle: statistical methods for analysing single cell RNA-seq data

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