Introduction | Installation | Quick Start with SummarizedExperiment | Load the package | Create a minimal object | Check passport on unstamped object | Log processing steps | Read the processing log | Stamping with interactive popup (Seurat workflow) | Logging Processing Steps | Custom Fields | Passport Fields Reference | Identity | Animal Info | Experiment Info | Lineage | Session Info
Package: scPassport 1.1.0
Sedat Kacar
scPassport: Passport System for Single-Cell Objects
Stamps Seurat, SingleCellExperiment, and SummarizedExperiment objects with a persistent metadata passport. For Seurat objects the passport is stored in the misc slot; for SingleCellExperiment and SummarizedExperiment objects it is stored in the metadata slot. Tracks animal info, experiment details, lineage (parent/child relationships), RDS registry numbers, processing logs, and custom fields. Includes an interactive Shiny gadget to fill and update the passport, and a read mode to print the full passport to console. The passport persists inside the RDS file with no external files needed.
Authors:
scPassport_1.1.0.tar.gz
scPassport_1.1.0.zip(r-4.7)scPassport_1.1.0.zip(r-4.6)scPassport_1.1.0.zip(r-4.5)
scPassport_1.1.0.tgz(r-4.6-x86_64)scPassport_1.1.0.tgz(r-4.6-arm64)scPassport_1.1.0.tgz(r-4.5-x86_64)scPassport_1.1.0.tgz(r-4.5-arm64)
scPassport_1.1.0.tar.gz(r-4.7-arm64)scPassport_1.1.0.tar.gz(r-4.7-x86_64)scPassport_1.1.0.tar.gz(r-4.6-arm64)scPassport_1.1.0.tar.gz(r-4.6-x86_64)
scPassport_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scPassport/json (API)
| # Install 'scPassport' in R: |
| install.packages('scPassport', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sedatkacar56/scpassport/issues
On BioConductor:scPassport-1.1.0(bioc 3.24)scPassport-1.0.0(bioc 3.23)
singlecelldataimportvisualizationinfrastructurecpp
Last updated from:b4e92ef543. Checks:12 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 186 | ||
| linux-devel-arm64 | NOTE | 197 | ||
| linux-devel-x86_64 | NOTE | 249 | ||
| source / vignettes | OK | 273 | ||
| linux-release-arm64 | NOTE | 188 | ||
| linux-release-x86_64 | NOTE | 270 | ||
| macos-release-arm64 | NOTE | 128 | ||
| macos-release-x86_64 | NOTE | 349 | ||
| macos-oldrel-arm64 | NOTE | 101 | ||
| macos-oldrel-x86_64 | NOTE | 333 | ||
| windows-devel | NOTE | 167 | ||
| windows-release | NOTE | 154 | ||
| windows-oldrel | NOTE | 174 | ||
| wasm-release | OK | 160 |
Exports:log_stepread_passportscPassport
Dependencies:base64encBiocGenericsbslibcachemclicommonmarkdigestfastmapfontawesomefsgenericsgluehtmltoolshttpuvjquerylibjsonlitelaterlifecyclemagrittrmemoisemimeminiUIotelpromisesR6rappdirsRcpprlangS4Vectorssassshinysourcetoolswithrxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Log a Processing Step to a Seurat, SingleCellExperiment, or SummarizedExperiment Object | log_step |
| Read the Passport of a Seurat, SingleCellExperiment, or SummarizedExperiment Object | read_passport |
| scPassport: Passport System for Single-Cell Objects | scPassport-package scPassport |
