CRAN/E | CpmERCCutoff

CpmERCCutoff

Calculation of Log2 Counts per Million Cutoff from ERCC Controls

Installation

About

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.

Key Metrics

Version 1.0.0
R ≥ 3.6
Published 2022-09-13 584 days ago
Needs compilation? no
License GPL (≥ 3)
CRAN checks CpmERCCutoff results
Language en-US

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Maintainer

Maintainer

Kristen Steenbergen

ksteenbergen@emmes.com

Authors

Tyler Grimes

aut

Travis L. Jensen

aut

Kristen Steenbergen

ctb / cre

The Emmes Company LLC

cph

(Copyright holder of CpmERCCutoff package (Copyright (C) 2022))

Johannes B. Goll

aut

Material

Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-develnot available

x86_64

r-releasenot available

x86_64

r-oldrelnot available

x86_64

Depends

R ≥ 3.6

Imports

stats
graphics

Suggests

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testthat ≥ 3.0.0