quantiseqr
Quantification of the Tumor Immune contexture from RNA-seq data
Bioconductor version: Release (3.20)
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")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.14.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | quantiseqr_1.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | quantiseqr_1.14.0.tgz |
| macOS Binary (arm64) | quantiseqr_1.13.0.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 |