Introduction | How to cite | Dependencies | Creating an MPRASet object | Tissue comparison | Allele comparison | Analysis | Allelic comparison | Returning an MPRASet | Session Info | References
Package: mpra 1.35.0
Leslie Myint
mpra: Analyze massively parallel reporter assays
Tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA).
Authors:
mpra_1.35.0.tar.gz
mpra_1.35.0.zip(r-4.7)mpra_1.35.0.zip(r-4.6)mpra_1.35.0.zip(r-4.5)
mpra_1.35.0.tgz(r-4.6-any)mpra_1.35.0.tgz(r-4.5-any)
mpra_1.35.0.tar.gz(r-4.7-any)mpra_1.35.0.tar.gz(r-4.6-any)
mpra_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mpra/json (API)
| # Install 'mpra' in R: |
| install.packages('mpra', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hansenlab/mpra/issues
Datasets:
- mpraSetAggExample - Example data for the mpra package.
- mpraSetAllelicExample - Example data for the mpra package.
- mpraSetExample - Example data for the mpra package.
On BioConductor:mpra-1.35.0(bioc 3.24)mpra-1.34.0(bioc 3.23)
softwaregeneregulationsequencingfunctionalgenomics
Last updated from:8dee10e44d. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 177 | ||
| linux-devel-x86_64 | NOTE | 319 | ||
| source / vignettes | OK | 230 | ||
| linux-release-x86_64 | NOTE | 349 | ||
| macos-release-arm64 | NOTE | 164 | ||
| macos-oldrel-arm64 | NOTE | 152 | ||
| windows-devel | NOTE | 193 | ||
| windows-release | NOTE | 201 | ||
| windows-oldrel | NOTE | 196 | ||
| wasm-release | OK | 122 |
Exports:compute_logratioget_precision_weightsgetBarcodegetDNAgetEidgetEseqgetRNAmpralmMPRASetnormalize_countsshow
Dependencies:abindBiobaseBiocGenericscliDelayedArrayfarvergenericsGenomicRangesglueIRangeslabelinglatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsR6RColorBrewerrlangS4ArraysS4VectorsscalesSeqinfoSparseArraystatmodSummarizedExperimentviridisLiteXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Analyze massively parallel reporter assays | mpra-package mpra |
| Compute activity measure (log-ratio) for each element. | compute_logratio |
| Get precision weights from the copy number-variance relationship. | get_precision_weights |
| Linear models for differential analysis of MPRA data | mpralm |
| Class '"MPRASet"' | getBarcode getDNA getEid getEseq getRNA MPRASet MPRASet-class show,MPRASet-method |
| Example data for the mpra package. | mpraSetAggExample mpraSetAllelicExample mpraSetExample |
| Total count normalization of DNA and RNA counts | normalize_counts |
