Simply copy and paste the 16S_rDNA_script_run file into the directory containing the 16S_RNA-seq_stats.R or 16S_rDNA_script_edt_compound_gene.R, otu_table_tax.spf, and mapping_file.txt files. Do not open this files in microsoft excel - libre office - google sheets!
No further installation is necessary.
Double click the 16S_rDNA_script_run file and select the R script to run. The open it. While it is running, a dialogue box will remain open. This box closes when the analysis has finished.
Other option is, instead, open the 16S_rDNA_script.R or 16S_rDNA_script_edt_compound_gene.R, select the script and modify the "/PATH/TO/WORK/DIRECTORY/".
Need to have R and the following packages installed through it:
- psych;
- pvclust;
- gplots;
- PMCMRplus;
- ggbiplot;
- vegan.
Development of the RNA-seq module:
- Cristal Villalba
- Luis Dias Soares
Review and testing:
- Cristal Villalba - Nucleo de Bioinformatica CPE/HCPA
- Luis Dias Soares - Nucleo de Bioinformatica CPE/HCPA
- Martiela Freitas - Nucleo de Bioinformatica CPE/HCPA
Supervision:
Ursula Matte - Nucleo de Bioinformatica CPE/HCPA
We thank for the finantial support of Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for the fellowships provided to GCVS (Process no.:148615/2018-0) MF (Process no.: 140002/2018-9), and UM (Process no.: 312714/2018-1). We also thank FIPE/HCPA for financial support.