R Observatory: Metrics for wTO version 2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

wTO

2.1Package record

Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network

1packages dependsuggested by 1

4.1Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Deisy Morselli GysiCRAN page ↗

Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at doi:10.1186/s12859-018-2351-7.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("wTO", 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-wto

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-wTO

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-wTO

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

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

Maintainer: ‘Deisy Morselli Gysi <deisy.ccnr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Deisy", "Morselli"),
                      family = "Gysi",
                      role = c("aut", "cre"),
                      email = "deisy.ccnr@gmail.com"),
               person(given = "Andre",
                      family = "Voigt",
                      role = "aut"),
               person(given = c("Tiago", "Miranda"),
                      family = "Fragoso",
                      role = "aut"),
               person(given = "Eivind",
                      family = "Almaas",
                      role = "aut"),
               person(given = "Katja",
                      family = "Nowick.",
                      role = "aut"))
as necessary.

CRAN check page ↗

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1

READMEYes · 15 wordsVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 17 (4 internal)
Examples that run: 17%1 run in a plain check · 4 never run · 1 hold no code
Exported functions with examples: 67%
Documented parameters: 98%
Return-value docs: 33%
Help pages citing references: 6%

How these are measured

Downloads

4.1K

CRAN downloads in the past year

Rank #9,725 · ~11/day · ~339/mo

Releases R versions

Daily download trend is not available in this view yet.

35130 days

1K90 days

4.1K1 year

Compare downloads with other packages →

Also on78 r2u6 autocran1.6K conda_forge59 c2d4u

How downloads are counted

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing wTO adds 46 packages (30 with compiled code, 51 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, bslib 5.6 MB.

Depends (0)

none

Imports (11)

data.table igraph magrittr plyrparallelsom visNetwork reshape2 Rfast HiClimRmethods

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

NetSci

Suggests, most downloaded first

CoDiNA

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (5)

Deisy Morselli Gysi

Andre Voigt

Tiago Miranda Fragoso

Eivind Almaas

Katja Nowick.

Maintainer since 1.1.0 (2017)

Releases (16)

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
unarchivedReturned to CRAN
2024-07-05
2.1Latest
record
2024-07-05 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-04-20
issues were not corrected despite reminders
R
R 4.3.0 released · 2023-04-21
2.0.2
record
2023-03-22 · diff ↗
2.0.1
record
2022-05-24 · diff ↗
2.0
record
2022-05-11 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.6.3
record
2018-11-17 · diff ↗
1.6.2
record
2018-10-14 · diff ↗ ·
added 1 export
wTO.rep_measure

Show 12 earlier eventsHide 12 earlier events

1.6.1
record
2018-06-28 · diff ↗ ·
removed 1 export
Correlation.Overlap

added 1 export
CorrelationOverlap
1.6
record
2018-05-30 · diff ↗ ·
added 1 export
wTO.fast
R
R 3.5.0 released · 2018-04-23
1.5
record
2018-03-02 · diff ↗ ·
added 1 export
wTO.export
1.4.2
record
2018-02-01 · diff ↗
1.4.1
record
2017-11-22 · diff ↗
1.4.0
record
2017-11-12 · diff ↗
1.3.0
record
2017-10-04 · diff ↗
1.2.2
record
2017-07-16 · diff ↗
1.2.0
record
2017-06-08 · diff ↗
1.1.0
record
2017-05-29
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-29
Total releases: 16 / 9 yrs
License: GPL-2 OSI
Bundled data: 149 KB / 4 files
Download size: 91 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("wTO")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 wTO version 2.1 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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