R Observatory: Metrics for VALERIE version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

VALERIE

1.1.0Package record

Visualising Splicing at Single-Cell Resolution

0packages depend

3.2Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Sean WenCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Sean Wen <sean.wenwx@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Sean",
                    family = "Wen",
                    role = c("aut", "cre"),
                    email = "sean.wenwx@gmail.com")
as necessary.

CRAN check page ↗

Slowest check: 8.7 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE11 OK, 2 NOTE2026-05-10

Show 4 earlier changesHide 4 earlier changes

ERROR10 OK, 2 NOTE, 1 ERROR2026-05-03
NOTE10 OK, 2 NOTE2026-04-25
ERROR9 OK, 4 NOTE, 1 ERROR2026-03-30
NOTE9 OK, 5 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 12
Examples that run: 100%12 run in a plain check
Exported functions with examples: 100%
Documented parameters: 88%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

VALERIE PDF

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #8,101 · ~9/day · ~265/mo

Releases R versions

Daily download trend is not available in this view yet.

29630 days

1.1K90 days

3.2K1 year

Compare downloads with other packages →

Also on130 r2u

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing VALERIE adds 76 packages (37 with compiled code, 67 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, doBy 4.3 MB. 4 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

People & History

People (from the free-text Author field) (1)

Sean Wen

Maintainer since 1.0.0 (2020)

Releases (2)

Pick two releases to compare their code metrics.

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
record
2020-07-10 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.0
record
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

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("VALERIE")

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for VALERIE version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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