Package: ECLIPSE 0.99.0

Ethan Burns

ECLIPSE: ECLIPSE: Enhanced CLonotypic Inference via Prediction of Single-cell Expression

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 objects and Cell Ranger vdj/multi contig files are required as inputs.

Authors:Ethan Burns [aut, cre], Zhaochen Ye [ctb], Kelly Street [ctb], David Braun [aut, fnd]

ECLIPSE_0.99.0.tar.gz
ECLIPSE_0.99.0.zip(r-4.7-any)ECLIPSE_0.99.0.zip(r-4.6-any)ECLIPSE_0.99.0.zip(r-4.5-any)
ECLIPSE_0.99.0.tgz(r-4.6-any)ECLIPSE_0.99.0.tgz(r-4.5-any)
ECLIPSE_0.99.0.tar.gz(r-4.7-any)ECLIPSE_0.99.0.tar.gz(r-4.6-any)
ECLIPSE_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ECLIPSE/json (API)

# Install 'ECLIPSE' in R:

install.packages('ECLIPSE', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/eburns10/eclipse/issues

Datasets:

post_qc_contigs - Example Post-QC TCR contigs that would be generated within ECLIPSE and passed to findThreeChainClones.
test_seurat - Example minimal Seurat object without TCR information.
test_seurat_with_tcr - Example Seurat object with TCR information generated by running the ECLIPSE function.
vignette_object - Example small Seurat object without TCR information.

On CRAN:

software geneexpression biomedicalinformatics immunooncology transcriptomics classification singlecell annotation sequencing

3.30 score 5 scripts 3 exports 144 dependencies

Last updated from:7f479a65a1. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	215
linux-devel	OK	311
source / vignettes	OK	306
linux-release	OK	383
macos-release	OK	255
macos-oldrel	OK	237
windows-devel	OK	290
windows-release	OK	265
windows-oldrel	OK	285
wasm-release	OK	182

Exports:ECLIPSE findThreeChainClones tcrDoubletDetect

Dependencies:abind askpass base64enc BH Biobase BiocGenerics BiocManager BiocParallel BiocStyle Biostrings bookdown brio bslib cachem callr cli codetools cowplot cpp11 crayon curl DelayedArray desc diffobj digest dotCall64 dplyr evaluate evmix farver fastmap fontawesome formatR fs futile.logger futile.options future future.apply generics GenomicRanges ggalluvial ggdendro ggforce ggplot2 ggraph ggrepel globals glue graphlayouts gridExtra gsl gtable highr htmltools httr igraph immApex immReferent iNEXT IRanges isoband jquerylib jsonlite knitr labeling lambda.r lattice lazyeval lifecycle listenv magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mime openssl otel parallelly pillar pkgbuild pkgconfig pkgload plyr polyclip praise processx progressr ps purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rjson rlang rmarkdown rprojroot rvest S4Arrays S4Vectors S7 sass scales scRepertoire selectr Seqinfo SeuratObject SingleCellExperiment snow sp spam SparseArray SparseM stringi stringr SummarizedExperiment survival sys systemfonts testthat tibble tidygraph tidyr tidyselect tinytex tweenr utf8 vctrs VDJdive viridis viridisLite waldo withr xfun xml2 XVector yaml

Introduction to ECLIPSE

Rendered fromECLIPSE.Rmdusingknitr::rmarkdown

Last update: 2026-08-11
Started: 2026-07-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Determines the true clonotype of each cell	ECLIPSE
Finds clones with 3 total TCR chains and modifies their contigs	findThreeChainClones
Example Post-QC TCR contigs that would be generated within ECLIPSE and passed to findThreeChainClones.	post_qc_contigs
Finds and removes doublets from Seurat objects	tcrDoubletDetect
Example minimal Seurat object without TCR information.	test_seurat
Example Seurat object with TCR information generated by running the ECLIPSE function.	test_seurat_with_tcr
Example small Seurat object without TCR information.	vignette_object