clippda
This is the development version of clippda; for the stable release version, see clippda.
A package for the clinical proteomic profiling data analysis
Bioconductor version: Development (3.24)
Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.
Author: Stephen Nyangoma
Maintainer: Stephen Nyangoma <s.o.nyangoma at bham.ac.uk>
citation("clippda")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("clippda")
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("clippda")| Sample Size Calculation | R Script | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, MultipleComparison, OneChannel, Preprocessing, Proteomics, Software |
| Version | 1.63.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (17 years) |
| License | GPL (>=2) |
| Depends | R (>= 2.13.1), limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods |
| Imports | |
| System Requirements | |
| URL | http://www.cancerstudies.bham.ac.uk/crctu/CLIPPDA.shtml |
See More
| Suggests | |
| 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 | clippda_1.63.0.tar.gz |
| Windows Binary (x86_64) | clippda_1.63.0.zip |
| macOS Binary (big-sur-x86_64) | clippda_1.63.0.tgz |
| macOS Binary (sonoma-arm64) | clippda_1.63.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/clippda |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/clippda |
| Bioc Package Browser | https://code.bioconductor.org/browse/clippda/ |
| Package Short Url | https://bioconductor.org/packages/clippda/ |
| Package Downloads Report | Download Stats |