Package: VALERIE 1.1.0

Sean Wen

VALERIE: Visualising Splicing at Single-Cell Resolution

Alternative splicing produces a variety of different protein products from a given gene. 'VALERIE' enables visualisation of alternative splicing events from high-throughput single-cell RNA-sequencing experiments. 'VALERIE' computes percent spliced-in (PSI) values for user-specified genomic coordinates corresponding to alternative splicing events. PSI is the proportion of sequencing reads supporting the included exon/intron as defined by Shiozawa (2018) <doi:10.1038/s41467-018-06063-x>. PSI are inferred from sequencing reads data based on specialised infrastructures for representing and computing annotated genomic ranges by Lawrence (2013) <doi:10.1371/journal.pcbi.1003118>. Computed PSI for each single cell are subsequently presented in the form of a heatmap implemented using the 'pheatmap' package by Kolde (2010) <https://CRAN.R-project.org/package=pheatmap>. Board overview of the mean PSI difference and associated p-values across different user-defined groups of single cells are presented in the form of a line graph using the 'ggplot2' package by Wickham (2007) <https://CRAN.R-project.org/package=ggplot2>.

Authors:Sean Wen

VALERIE_1.1.0.tar.gz
VALERIE_1.1.0.tar.gz(r-4.5-noble)VALERIE_1.1.0.tar.gz(r-4.4-noble)
VALERIE_1.1.0.tgz(r-4.4-emscripten)VALERIE_1.1.0.tgz(r-4.3-emscripten)
VALERIE.pdf |VALERIE.html✨
VALERIE/json (API)

# Install 'VALERIE' in R:
install.packages('VALERIE', repos = 'https://cloud.r-project.org')

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.30 score 137 downloads 2 mentions 12 exports 114 dependencies

Last updated 5 years agofrom:1bdf7ed399. Checks:1 OK, 2 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 19 2025
R-4.5-linuxWARNINGMar 19 2025
R-4.4-linuxWARNINGMar 19 2025

Exports:ComputePSIPlotPSIPlotPSI.A3SS.MultiGroupsPlotPSI.A3SS.TwoGroupsPlotPSI.A5SS.MultiGroupsPlotPSI.A5SS.TwoGroupsPlotPSI.MXE.MultiGroupsPlotPSI.MXE.TwoGroupsPlotPSI.RI.MultiGroupsPlotPSI.RI.TwoGroupsPlotPSI.SE.MultiGroupsPlotPSI.SE.TwoGroups

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbootbroomcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crayoncurlDelayedArrayDerivdigestdoBydplyrfansifarverformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggplotifyggpubrggrepelggsciggsignifgluegridExtragridGraphicsgtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpheatmappillarpkgconfigplyrpolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasRhtslibrlangRsamtoolsrstatixS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectoryulab.utils

VALERIE

Sean Wen

Rendered fromVALERIE.Rmdusingknitr::rmarkdownon Mar 19 2025.

Last update: 2020-07-10
Started: 2020-02-11

Citation

To cite package ‘VALERIE’ in publications use:

Wen S (2020). VALERIE: Visualising Splicing at Single-Cell Resolution. R package version 1.1.0, https://CRAN.R-project.org/package=VALERIE.

ATTENTION: This citation information has been auto-generated from the package DESCRIPTION file and may need manual editing, see ‘help("citation")’.

Corresponding BibTeX entry: 

  @Manual{,
    title = {VALERIE: Visualising Splicing at Single-Cell Resolution},
    author = {Sean Wen},
    year = {2020},
    note = {R package version 1.1.0},
    url = {https://CRAN.R-project.org/package=VALERIE},
  }