Introduction | What is ECLIPSE? Why should I use it to analyze my scTCR-seq data? | What are the inputs to ECLIPSE? Is there any pre-processing required? | How is ECLIPSE different from other Bioconductor and non-Bioconductor scTCR-seq analysis packages? | Installation and loading | Test dataset | Preparing inputs for ECLIPSE | Contig files | Option 1: use folder paths | Option 2: use contig file paths | Seurat object meta.data | Column to pass to original_barcode | Column to pass to batch | Column to pass to donor | Column to pass to group | Running the ECLIPSE function | Description of function | Running ECLIPSE | Running tcrArtifactDetect | Downstream analysis with r Biocpkg("scRepertoire") | Conclusions | Supplemental information | Using ECLIPSE without a Seurat object | SingleCellExperiment objects | Other objects | Helper function: findThreeChainClones | ECLIPSE additional arguments | Seurat object columns description | Session info
Package: ECLIPSE 0.99.3
Ethan Burns
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/SingleCellExperiment objects and Cell Ranger vdj/multi contig files are required as inputs.
Authors:
ECLIPSE_0.99.3.tar.gz
ECLIPSE_0.99.3.zip(r-4.7-any)ECLIPSE_0.99.3.zip(r-4.6-any)ECLIPSE_0.99.3.zip(r-4.5-any)
ECLIPSE_0.99.3.tgz(r-4.6-any)ECLIPSE_0.99.3.tgz(r-4.5-any)
ECLIPSE_0.99.3.tar.gz(r-4.7-any)ECLIPSE_0.99.3.tar.gz(r-4.6-any)
ECLIPSE_0.99.3.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://bioc.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.
- unit_test_object - Example small Seurat object without TCR information used for unit testing.
- vignette_object - Example small Seurat object without TCR information.
softwaregeneexpressionbiomedicalinformaticsimmunooncologytranscriptomicsclassificationsinglecellannotationsequencing
Last updated from:9ca87aa15b. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 222 | ||
| linux-devel | OK | 455 | ||
| source / vignettes | OK | 346 | ||
| linux-release | OK | 402 | ||
| macos-release | OK | 248 | ||
| macos-oldrel | OK | 319 | ||
| windows-devel | OK | 403 | ||
| windows-release | OK | 424 | ||
| windows-oldrel | OK | 426 | ||
| wasm-release | OK | 139 |
Exports:ECLIPSEfindThreeChainClonessceECLIPSEtcrArtifactDetect
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringscachemclicodetoolscowplotcpp11crayoncurlDelayedArraydotCall64dplyrevmixfarverfastmapformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesggalluvialggdendroggforceggplot2ggraphggrepelglobalsgluegraphlayoutsgridExtragslgtablehttrigraphimmApeximmReferentiNEXTIRangesisobandjsonlitelabelinglambda.rlatticelazyevallifecyclelistenvmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemimeopensslparallellypillarpkgconfigplyrpolyclipprogressrpurrrquantregR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rjsonrlangrvestS4ArraysS4VectorsS7scalesscRepertoireselectrSeqinfoSeuratObjectSingleCellExperimentsnowspspamSparseArraySparseMstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsVDJdiveviridisviridisLitewithrxml2XVectoryaml
