CpmERCCutoff

1.0.0

Calculation of Log2 Counts per Million Cutoff from ERCC Controls

0packages depend

7.9Kdownloads / year

49.4%test coverage

12/13checks pass

Overview

About

Maintained by Kristen SteenbergenFirst published 2022-09-131 releasesCRAN page ↗

Implementation of the empirical method to derive log2 counts per million (CPM) cutoff to filter out lowly expressed genes using ERCC spike-ins as described in Goll and Bosinger et.al (2022)doi:10.1101/2022.06.23.497396. This package utilizes the synthetic mRNA control pairs developed by the External RNA Controls Consortium (ERCC) (ERCC 1 / ERCC 2) that are spiked into sample pairs at known ratios at various absolute abundances. The relationship between the observed and expected fold changes is then used to empirically determine an optimal log2 CPM cutoff for filtering out lowly expressed genes.

Install

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

install.packages("CpmERCCutoff", 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-cpmerccutoff

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-CpmERCCutoff

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-CpmERCCutoff

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

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 59 s · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.11

49.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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: 100%
Return-value docs: 100%
References docs: 0%

Downloads

7.9K

CRAN downloads in the past year

Rank #5,598 · ~22/day · ~660/mo

Releases R versions

Daily download trend is not available in this view yet.

21130 days

1.5K90 days

7.9K1 year

Compare downloads with other packages →

Also on115 r2u2 autocran

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6

Imports (2)

statsgraphics

LinkingTo (0)

none

Suggests (2)

spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Kristen Steenbergen

Contributor, Maintainer

Authors (3)

Johannes B. Goll

Author

Tyler Grimes

Author

Travis L. Jensen

Author

Contributors (1)

Kristen Steenbergen

Contributor, Maintainer

The Emmes Company LLC

Listed in earlier versions (2)

Johannes B.

no longer listed · 1.0.0

Travis L.

no longer listed · 1.0.0

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2022-09-13
Total releases: 1 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.6
Bundled data: 26 KB / 3 files
Download size: 52 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →