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CpmERCCutoff  

Calculation of Log2 Counts per Million Cutoff from ERCC Controls
View on CRAN: Click here


Download and install CpmERCCutoff package within the R console
Install from CRAN:
install.packages("CpmERCCutoff")

Install from Github:
library("remotes")
install_github("cran/CpmERCCutoff")

Install by package version:
library("remotes")
install_version("CpmERCCutoff", "1.0.0")



Attach the package and use:
library("CpmERCCutoff")
Maintained by
Kristen Steenbergen
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-09-13
Latest Update: 2022-09-13
Description:
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). 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.
How to cite:
Kristen Steenbergen (2022). CpmERCCutoff: Calculation of Log2 Counts per Million Cutoff from ERCC Controls. R package version 1.0.0, https://cran.r-project.org/web/packages/CpmERCCutoff
Previous versions and publish date:
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Other R packages that CpmERCCutoff depends, imports, suggests or enhances
Functions, R codes and Examples using the CpmERCCutoff R package
Some associated functions: exp_input . getLowLcpmCutoff . mta_dta . obs_input . plot.empLCPM . print.empLCPM . summary.empLCPM . 
Some associated R codes: data.R . getLowLcpmCutoff.R . imports.R .  Full CpmERCCutoff package functions and examples
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