func2vis

1.0-3

Clean and Visualize Over Expression Results from 'ConsensusPathDB'

0packages depend

3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Raghvendra MallFirst published 2020-08-103 releasesCRAN page ↗

Provides functions to have visualization and clean-up of enriched gene ontologies (GO) terms, protein complexes and pathways (obtained from multiple databases) using 'ConsensusPathDB' from gene set over-expression analysis. Performs clustering of pathway based on similarity of over-expressed gene sets and visualizations similar to Ingenuity Pathway Analysis (IPA) when up and down regulated genes are known. The methods are described in a paper currently submitted by Orecchioni et al, 2020 in Nanoscale.

Install

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

install.packages("func2vis", 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-func2vis

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

# 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-func2vis

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-func2vis

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 30%

Downloads

CRAN downloads in the past year

Rank #14,384 · ~8/day · ~248/mo

Releases R versions

Daily download trend is not available in this view yet.

24630 days

74190 days

3K1 year

Compare downloads with other packages →

Also on408 r2u22 autocran22 c2d4u

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (7)

R >= 4.0ggplot2 igraph devtools ggrepelgrDevicesrandomcoloR

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Raghvendra Mall

Author, Maintainer

Authors (1)

Raghvendra Mall

Author, Maintainer

Package Timeline

3 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
1.0-3Latest
2023-03-16 · current release · diff ↗
1.0-2
2022-08-29 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0-1
2020-08-10
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-08-10
Total releases: 3 / 6 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0
Bundled data: 223 KB / 4 files
Download size: 233 KB
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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