training: Training data
In santiago1234/iCodon: iCodon: Designing "ideal" coding (iCodon) sequences for customized expression level
training R Documentation
Training data
Description
This is the data used to train the predictive model
Usage
training
Format
A data frame with 67,775 rows and 8 variables:
- gene_id
Ensembl gene id
- specie
The specie one of: human, fish, mouse, or xenopus
- cell_type
The cell type: 293t, embryo mz, hela, mES cells, k562, or RPE
- datatype
experimental technique used to obtain the mRNA stability measurements (decay rate)
- decay_rate
The decay rate (variable to predict), scaled with respect to each experiment
- utrlenlog
size in log scale of the 5' UTR
- coding
coding dna sequence in frame
- cdslenlog
size in log scale of the coding sequence
Details
The decay rate measurements were obtained from the following papers:
Bazzini, Ariel A., et al. "Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition."
Wu, Qiushuang, et al. "Translation affects mRNA stability in a codon-dependent manner in human cells." Elife 8 (2019): e45396.
Herzog, Veronika A., et al. "Thiol-linked alkylation of RNA to assess expression dynamics." Nature methods 14.12 (2017): 1198.
santiago1234/iCodon documentation built on Nov. 2, 2023, 2:03 p.m.
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| training | R Documentation |
Training data
Description
This is the data used to train the predictive model
Usage
training
Format
A data frame with 67,775 rows and 8 variables:
- gene_id
Ensembl gene id
- specie
The specie one of: human, fish, mouse, or xenopus
- cell_type
The cell type: 293t, embryo mz, hela, mES cells, k562, or RPE
- datatype
experimental technique used to obtain the mRNA stability measurements (decay rate)
- decay_rate
The decay rate (variable to predict), scaled with respect to each experiment
- utrlenlog
size in log scale of the 5' UTR
- coding
coding dna sequence in frame
- cdslenlog
size in log scale of the coding sequence
Details
The decay rate measurements were obtained from the following papers:
Bazzini, Ariel A., et al. "Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition."
Wu, Qiushuang, et al. "Translation affects mRNA stability in a codon-dependent manner in human cells." Elife 8 (2019): e45396.
Herzog, Veronika A., et al. "Thiol-linked alkylation of RNA to assess expression dynamics." Nature methods 14.12 (2017): 1198.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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