Computational tools from Pedro H. Oliveira

Some useful links

Epigenomic workflows

Semi-automated Bash workflows for epigenomic analyses: RNA-seq, SMRT-seq, methylation motif analyses, etc. Include a step-by-step tutorial and a link to run each pipeline module via Docker.

HMM profiles for detection of restriction-modification systems

HMM profiles for detection of Types I, II, IIC, III, and IV restriction endonucleases and methyltransferases.

Useful bash/python/perl one-liners for bioinformatics

List of basic commands for handling and parsing common file types (e.g. FASTA/Q, SAM, BAM, etc), word exceptionality, among others. Great for beginners!

Useful bash/python/R scripts for bioinformatics and beyond

Miscellaneous scripts for multiple purposes (e.g.: DNA walks, Shannon entropy, file encryption).

If you are interested in any of these tools, please contact Pedro H. Oliveira for more information.

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