title: "OmicsChrono: temporal metadata for longitudinal omics"author: "Mateo Pedersen"date: "r Sys.Date()"output: BiocStyle::html_documentvignette: >%\VignetteIndexEntry | Introduction | Relationship to existing Bioconductor software | Real RNA-seq time-course data | Civil timestamps and daylight saving | Zeitgeber time and photoperiod | Analysis-ready design data | Limitations | Session information
Package: OmicsChrono 0.99.0
Mateo Pedersen
OmicsChrono: Calendar-Aware Temporal Metadata for Longitudinal Omics
Longitudinal and circadian omics experiments encode sample time as elapsed experiment time, civil timestamps, or light-cycle coordinates. OmicsChrono validates and standardizes temporal sample metadata in SummarizedExperiment and derived Bioconductor containers while preserving assays and feature metadata. It supports elapsed-time annotation, sampling-window alignment, time-zone and daylight-saving diagnostics, Zeitgeber-time annotation, and temporal coverage summaries as reproducible preprocessing for downstream time-course analyses.
Authors:
OmicsChrono_0.99.0.tar.gz
OmicsChrono_0.99.0.zip(r-4.7-any)OmicsChrono_0.99.0.zip(r-4.6-any)OmicsChrono_0.99.0.zip(r-4.5-any)
OmicsChrono_0.99.0.tgz(r-4.6-any)OmicsChrono_0.99.0.tgz(r-4.5-any)
OmicsChrono_0.99.0.tar.gz(r-4.7-any)OmicsChrono_0.99.0.tar.gz(r-4.6-any)
OmicsChrono_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OmicsChrono/json (API)
| # Install 'OmicsChrono' in R: |
| install.packages('OmicsChrono', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mateopedersen/omicschrono/issues
softwaretimecoursepreprocessing
Last updated from:959908a08a. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 148 | ||
| linux-devel | OK | 190 | ||
| source / vignettes | OK | 204 | ||
| linux-release | OK | 151 | ||
| macos-release | OK | 118 | ||
| macos-oldrel | OK | 108 | ||
| windows-devel | OK | 99 | ||
| windows-release | OK | 91 | ||
| windows-oldrel | OK | 104 | ||
| wasm-release | OK | 99 |
Exports:addZeitgeberTimealignSampleTimesannotateSampleTimetemporalCoveragetemporalDesignDatavalidateSampleTime
Dependencies:abindBiobaseBiocGenericscliclockcpp11DelayedArraygenericsGenomicRangesglueIRangeslatticelifecycleMatrixMatrixGenericsmatrixStatsrlangS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimenttzdbvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add Zeitgeber and photoperiod annotations | addZeitgeberTime |
| Align observed sample times to expected sampling windows | alignSampleTimes |
| Annotate a SummarizedExperiment with normalized sample time | annotateSampleTime |
| Summarize temporal coverage | temporalCoverage |
| Construct explicit temporal design covariates | temporalDesignData |
| Validate temporal sample metadata | validateSampleTime |
