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VALERIE
View on CRAN: Click
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Download and install VALERIE package within the R console
Install from CRAN:
install.packages("VALERIE")
Install from Github:
library("remotes")
install_github("cran/VALERIE")
Install by package version:
library("remotes")
install_version("VALERIE", "1.1.0")
Attach the package and use:
library("VALERIE")
Maintained by
Sean Wen
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[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-02-11
Latest Update: 2020-07-10
Description:
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>.
How to cite:
Sean Wen (2020). VALERIE: Visualising Splicing at Single-Cell Resolution. R package version 1.1.0, https://cran.r-project.org/web/packages/VALERIE. Accessed 07 Nov. 2024.
Previous versions and publish date:
1.0.0 (2020-02-11 11:40)
Other packages that cited VALERIE R package
View VALERIE citation profile
Other R packages that VALERIE depends,
imports, suggests or enhances
Complete documentation for VALERIE
Functions, R codes and Examples using
the VALERIE R package
Some associated functions: ComputePSI . PlotPSI.A3SS.MultiGroups . PlotPSI.A3SS.TwoGroups . PlotPSI.A5SS.MultiGroups . PlotPSI.A5SS.TwoGroups . PlotPSI.MXE.MultiGroups . PlotPSI.MXE.TwoGroups . PlotPSI.RI.MultiGroups . PlotPSI.RI.TwoGroups . PlotPSI.SE.MultiGroups . PlotPSI.SE.TwoGroups . PlotPSI .
Some associated R codes: Script_VALERIE_ComputePSI.R . Script_VALERIE_PlotPSI.R . Script_VALERIE_PlotPSI_A3SS_MultiGroups.R . Script_VALERIE_PlotPSI_A3SS_TwoGroups.R . Script_VALERIE_PlotPSI_A5SS_MultiGroups.R . Script_VALERIE_PlotPSI_A5SS_TwoGroups.R . Script_VALERIE_PlotPSI_MXE_MultiGroups.R . Script_VALERIE_PlotPSI_MXE_TwoGroup.R . Script_VALERIE_PlotPSI_RI_MultiGroups.R . Script_VALERIE_PlotPSI_RI_TwoGroups.R . Script_VALERIE_PlotPSI_SE_MultiGroups.R . Script_VALERIE_PlotPSI_SE_TwoGroups.R . Full VALERIE package functions and examples
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