Custom codes for Hayashi et al. (2018)

This repository includes custom R and Julia codes for generating and processing of the data described in:

• Tetsutaro Hayashi†, Haruka Ozaki†, Yohei Sasagawa, Mana Umeda, Hiroki Danno and Itoshi Nikaido, Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, accepted.

Citation

Tetsutaro Hayashi, Haruka Ozaki, Yohei Sasagawa, Mana Umeda, Hiroki Danno and Itoshi Nikaido, Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, accepted.

License

Copyright (c) 2017 Haruka Ozaki Released under the MIT license

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Brief description of custom codes

Analysis of recursive splicing (Fig. 4, Supplementary Fig. 16 and 17)

The directory recursive_splicing includes custom codes for preparing of coverage data, fitting sawtooth patterns, replotting fitted data, and calculating RS detection probability.

Analysis of enahncer RNA (Fig. 5, Supplementary Fig. 18 and 19)

The directory enhancer_rna includes custom codes for generating aggregation plots and heatmaps from output files of deepTools.

Millefy (Fig. 3e and 4bc, Supplementary Fig. 10)

millefy, Genome browser-like visualization of single-cell RNA-seq dataset, is available from https://github.com/yuifu/millefy.