supp_figure2e: Conding potential analysis via CPC.

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 3 rows and 10 variables:

'Transcript name'

http://cpc.cbi.pku.edu.cn/docs/quick_guide.jsp

Coding

http://cpc.cbi.pku.edu.cn/docs/quick_guide.jsp

'Coding Potential Score'

http://cpc.cbi.pku.edu.cn/docs/quick_guide.jsp

'Hit number'

http://cpc.cbi.pku.edu.cn/docs/quick_guide.jsp

'Hit score'

http://cpc.cbi.pku.edu.cn/docs/quick_guide.jsp

'Frame score'

http://cpc.cbi.pku.edu.cn/docs/quick_guide.jsp

Length

http://cpc.cbi.pku.edu.cn/docs/quick_guide.jsp

'Coverage'

http://cpc.cbi.pku.edu.cn/docs/quick_guide.jsp

'Log-Odds score'

http://cpc.cbi.pku.edu.cn/docs/quick_guide.jsp

Type

http://cpc.cbi.pku.edu.cn/docs/quick_guide.jsp

...

Source

http://cpc.cbi.pku.edu.cn

Examples

getData('Supplementary Figure 2e')

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