quantiseqr
This is the development version of quantiseqr; for the stable release version, see quantiseqr.
Quantification of the Tumor Immune contexture from RNA-seq data
Bioconductor version: Development (3.24)
This package provides a streamlined workflow for the quanTIseq method, developed to perform the quantification of the Tumor Immune contexture from RNA-seq data. The quantification is performed against the TIL10 signature (dissecting the contributions of ten immune cell types), carefully crafted from a collection of human RNA-seq samples. The TIL10 signature has been extensively validated using simulated, flow cytometry, and immunohistochemistry data.
Author: Federico Marini [aut, cre]
, Francesca Finotello [aut]
Maintainer: Federico Marini <marinif at uni-mainz.de>
citation("quantiseqr")):
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("quantiseqr")
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("quantiseqr")| Using quantiseqr | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Classification, ExperimentHubSoftware, FeatureExtraction, FlowCytometry, GeneExpression, ImmunoOncology, Microarray, Sequencing, Software, StatisticalMethod, Transcription, Transcriptomics, Visualization |
| Version | 1.21.1 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0) |
| Imports | Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils |
| System Requirements | |
| URL |
See More
| Suggests | AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | easier |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | quantiseqr_1.21.1.tar.gz |
| Windows Binary (x86_64) | quantiseqr_1.21.1.zip |
| macOS Binary (big-sur-x86_64) | quantiseqr_1.21.1.tgz |
| macOS Binary (sonoma-arm64) | quantiseqr_1.21.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/quantiseqr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/quantiseqr |
| Bioc Package Browser | https://code.bioconductor.org/browse/quantiseqr/ |
| Package Short Url | https://bioconductor.org/packages/quantiseqr/ |
| Package Downloads Report | Download Stats |