ECLIPSE

This is the development version of ECLIPSE; to use it, please install the devel version of Bioconductor.

Enhanced CLonotypic Inference via Prediction of Single-cell Expression

Bioconductor version: Development (3.24)

This package is used for the analysis of single-cell T cell receptor sequencing data (scTCR-seq). ECLIPSE maps chain pairings across a sample to predict the true clonotype of each cell, unlike other methods which only consider the chains that are sequenced in each cell. Seurat/SingleCellExperiment objects and Cell Ranger vdj/multi contig files are required as inputs.

Author: Ethan Burns [aut, cre] ORCID: 0009-0009-8061-3686 , Zhaochen Ye [ctb] ORCID: 0009-0000-4422-3861 , Kelly Street [ctb] ORCID: 0000-0001-6379-5013 , David Braun [aut, fnd] ORCID: 0000-0003-4543-5553

Maintainer: Ethan Burns <ethan.burns at yale.edu>

Citation (from within R, enter citation("ECLIPSE")):

Ethan Burns, David Braun. ECLIPSE: Enhanced CLonotypic Inference via Prediction of Single-cell Expression. doi:10.18129/B9.bioc.ECLIPSE, R package version 0.99.3, https://bioconductor.org/packages/ECLIPSE.

Generated from the package metadata; it may differ from the package's own citation.

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("ECLIPSE")

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("ECLIPSE")

ECLIPSE	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, BiomedicalInformatics, Classification, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software, Transcriptomics
Version	0.99.3
In Bioconductor since	BioC 3.24 (R-4.6)
License	GPL (>= 3)
Depends	R (>= 4.4.0)
Imports	dplyr, ggplot2, scRepertoire, stringr, tidyr, VDJdive, methods, rlang, tidyselect, magrittr, utils
System Requirements
URL	https://github.com/eburns10/ECLIPSE
Bug Reports	https://github.com/eburns10/ECLIPSE/issues

Suggests	knitr, rmarkdown, ragg, tidyverse, testthat, BiocStyle, Seurat, SingleCellExperiment, S4Vectors, SummarizedExperiment, SeuratObject, tibble
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ECLIPSE_0.99.3.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/ECLIPSE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ECLIPSE
Package Short Url	https://bioconductor.org/packages/ECLIPSE/
Package Downloads Report	Download Stats