Cryptococcus neoformans transcriptome and translatome analysis 2018-2020.
Edward Wallace (Edward.Wallace@ed.ac.uk), Corinne Maufrais, Guilhem Janbon.
This work is the analysis, including most figure construction, for the paper:
Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom Wallace, Edward; Maufrais, Corinne ; Sales-Lee, Jade; Tuck, Laura; de Oliveira, Luciana; Feuerbach, Frank; Moyrand, Frédérique; Natarajan, Prashanthi; Madhani, Hiten; Janbon, Guilhem. Nucleic Acids Research, 2020 (in press)
A preprint of this work is on biorxiv: https://doi.org/10.1101/654046
Please cite the paper if you refer to or re-use any of this code.
This repository contains the code used for figures in the paper. It also contains additional figures that didn't make it into the paper, f incomplete or unsuccessful analyses, and so on. We are sharing it here as-is because it is better to work open.
Code is reusable under an Apache 2.0 Licence https://www.apache.org/licenses/LICENSE-2.0
ATG Context and translation analysis in Cryptococcus neoformans H99 and Cryptococcus deneoformans JEC21.
This contains R markdown files .Rmd format, making cryptococcus-centric figures in the paper.
ATG Context and translation analysis in other model fungi: Saccharomyces cerevisiae, Candida albicans, Schizosaccharomyces pombe, Neurospora crassa.
This contains R markdown files .Rmd format, making species-comparison files in the paper.
Coding sequence fasta files for Cryptococcus
Coding sequence fasta files for other model fungi
Annotation/ genome feature files gff3 for Cryptococcus
Annotation/ genome feature files gff3 for other model fungi
DESeq2 differential expression data on delta-upf1 vs wildtype JEC21.
Some svg-format files of sequence logos etc.
Protein sequence fasta files for Cryptococcus
Protein sequence fasta files for other model fungi
SharedScripts/sharedScripts.R contains R functions that are used in analyses, collected together into a single source file.
Code to run RiboCode for ORF analysis on Cryptococcus. Not completely successful and didn't reach the paper.
Upstream ORF analysis, both sequence fasta and genome feature files. Not completely successful and didn't reach the paper.