VALERIE

1.1.0

Visualising Splicing at Single-Cell Resolution

0packages depend

2.7Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Sean WenFirst published 2020-02-112 releasesCRAN page ↗

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.

Install

R (CRAN)Ubuntu (r2u)

install.packages("VALERIE", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-valerie

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 11.6 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-10
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-25
10 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-03-30
9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 88%
Return-value docs: 100%
References docs: 0%

Downloads

2.7K

CRAN downloads in the past year

Rank #13,402 · ~7/day · ~226/mo

Releases R versions

Daily download trend is not available in this view yet.

25830 days

80890 days

2.7K1 year

Compare downloads with other packages →

Also on203 r2u

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (10)

GenomicAlignments GenomicRanges IRanges Rsamtools plyr ggplot2 pheatmap ggplotify ggpubr scales

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (1)

Sean Wen

no longer listed · 1.0.0 to 1.1.0

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.0Latest
2020-07-10 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.0
2020-02-11
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-02-11
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Download size: 4.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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