figure1f: Conding potential analysis via CPAT.

In GranderLab/miR34a_asRNA_project: The miR34AasRNAproject package facilitates the transparency and reproducibility of the miR34a asRNA project and associated publication.

Description

Protein-coding capacity was evaluated using the Coding-potential Assessment Tool https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616698/ and Coding-potential Calculator https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933232/ with default settings. Transcript sequences for use with Coding-potential Assessment Tool were downloaded from the UCSC genome browser using the following IDs: HOTAIR (ENST00000455246.1), XIST (ENST00000429829.1), <ce><b2>-actin (ENST00000331789.5), Tubulin (ENST00000427480.1), and MYC (ENST00000377970). Transcript sequences for use with Coding-potential Calculator were downloaded from the UCSC genome browser using the following IDs: HOTAIR (uc031qho.1), <ce><b2>-actin (uc003soq.4).

Format

A tibble with 6 rows and 7 variables:

sequenceName

http://rna-cpat.sourceforge.net

RNAsize

http://rna-cpat.sourceforge.net

ORFsize

http://rna-cpat.sourceforge.net

FicketScore

http://rna-cpat.sourceforge.net

hexamerScore

http://rna-cpat.sourceforge.net

codingProbability

http://rna-cpat.sourceforge.net

codingLabel

http://rna-cpat.sourceforge.net

...

Source

http://lilab.research.bcm.edu/cpat/

Examples

getData('Figure 1f')

GranderLab/miR34a_asRNA_project documentation built on May 26, 2019, 7:26 a.m.