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quantiseqr
This is thereleased version of quantiseqr; for the devel version, seequantiseqr.
Quantification of the Tumor Immune contexture from RNA-seq data
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0003-3252-7758, Francesca Finotello [aut] ORCID: 0000-0003-0712-4658
Maintainer: Federico Marini <marinif at uni-mainz.de>
citation("quantiseqr")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("quantiseqr")For older versions of R, please refer to the appropriateBioconductor 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 | 1.18.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | quantiseqr_1.18.0.tar.gz |
| Windows Binary (x86_64) | quantiseqr_1.18.0.zip |
| macOS Binary (x86_64) | quantiseqr_1.18.0.tgz |
| macOS Binary (arm64) | quantiseqr_1.18.0.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 |