Protocols of the analyses performed for the PlanExp web application.
First, some data files that are too big to store in the git repository must be downloaded. Use the following commands.
cd PlanExp-protocols
chmod a+x src/*
src/download_data.sh
The analyses for the RNA-seq experiments (traditional RNA-seq and Single-Cell RNA-seq) can be found in the markdown/ directory.
The protocol for inferring gene co-expression relationships/gene regulatory interactions using GRNBoost can be found here.
S. Castillo-Lara, E. Pascual-Carreras, J.F. Abril
PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources
Bioinformatics, AOP 2019, doi:10.1093/bioinformatics/btz802
- Castillo-Lara, S. and Abril, J. F. (2018). PlanNET: homology-based predicted interactome for multiple planarian transcriptomes. Bioinformatics, 34(6), 1016–1023.
- Fincher, C. T. et al. (2018). Cell type transcriptome atlas for the planarian Schmidtea mediterranea. Science, 360(6391).
- Kao, D. et al. (2013). The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios. BMC Genomics, 14(1), 797.
- Labbé, R. M. et al. (2012). A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells, 30(8), 1734–1745.
- Plass, M. et al. (2018). Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics. Science, 360(6391).
- Rodríguez-Esteban, G. et al. (2015). Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. BMC Genomics, 16(1), 361.
- Sandmann, T. et al. (2011). The head-regeneration transcriptome of the planarian Schmidtea mediterranea. Genome Biology, 12(8), R76.