cellmigRation
This is the released version of cellmigRation; for the devel version, see cellmigRation.
Track Cells, Analyze Cell Trajectories and Compute Migration Statistics
Bioconductor version: Release (3.23)
Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions.
Author: Salim Ghannoum [aut, cph], Damiano Fantini [aut, cph], Waldir Leoncio [cre, aut], Øystein Sørensen [aut]
Maintainer: Waldir Leoncio <w.l.netto at medisin.uio.no>
citation("cellmigRation")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cellmigRation")
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("cellmigRation")| cellmigRation | HTML | R Script |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | CellBiology, DataImport, DataRepresentation, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-2 |
| Depends | R (>= 4.1), methods, foreach |
| Imports | tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc |
| System Requirements | |
| URL | https://github.com/ocbe-uio/cellmigRation/ |
| Bug Reports | https://github.com/ocbe-uio/cellmigRation/issues |
See More
| Suggests | knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl |
| 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 | cellmigRation_1.20.0.tar.gz |
| Windows Binary (x86_64) | cellmigRation_1.20.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | cellmigRation_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | cellmigRation_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cellmigRation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cellmigRation |
| Bioc Package Browser | https://code.bioconductor.org/browse/cellmigRation/ |
| Package Short Url | https://bioconductor.org/packages/cellmigRation/ |
| Package Downloads Report | Download Stats |