Sconify
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Sconify.
A toolkit for performing KNN-based statistics for flow and mass cytometry data
Bioconductor version: 3.9
This package does k-nearest neighbor based statistics and visualizations with flow and mass cytometery data. This gives tSNE maps"fold change" functionality and provides a data quality metric by assessing manifold overlap between fcs files expected to be the same. Other applications using this package include imputation, marker redundancy, and testing the relative information loss of lower dimension embeddings compared to the original manifold.
Author: Tyler J Burns
Maintainer: Tyler J Burns <burns.tyler at gmail.com>
citation("Sconify")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Sconify")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Sconify")| Data Quality | HTML | R Script |
| Final Post-Processing Steps for Scone | HTML | R Script |
| Finding Ideal K | HTML | R Script |
| General Scone Analysis | HTML | R Script |
| How to process FCS files for downstream use in R | HTML | R Script |
| Reference Manual |
Details
| biocViews | FlowCytometry, ImmunoOncology, MultipleComparison, SingleCell, Software, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5) |
| Imports | tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Sconify_1.4.0.tar.gz |
| Windows Binary | Sconify_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | Sconify_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Sconify |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Sconify |
| Bioc Package Browser | https://code.bioconductor.org/browse/Sconify/ |
| Package Short Url | https://bioconductor.org/packages/Sconify/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |