A collection of useful R tools for running DESeq2 on your data. This code is available in the Nature Protocol Exchange and includes the R script and several example input files. The associated publication is pending.
A collection of useful R methods for analyzing microbiome data. Includes methods for rarefication of 16S data, diversity metrics, differential abundance analysis and more. Code and example inputs are available in the Nature Protocol Exchange. This code is associated with the publication:
Nematode.net is a website dedicated to the dissemination of roundworm information to the community of Helminth scientists. This site provides users an interface enabling users to search for multifactorial combinations of species-omics properties associated with 73 nematode species.
Trematode.net is a website dedicated to the dissemination of flatworm information to the community of Helminth scientists. This site provides users an interface enabling users to search for multifactorial combinations of species-omics properties associated with 17 trematode species.
modDFS is a tool enabling users to assess Kegg module completeness. modDFS is available at SourceForge.net by following the ‘modDFS’ link above.
The ‘Genomics’ section of the handbook from our 2015 Bioinformatics Workshop for Helminth Genomics:
The ‘Transcriptome’ section of the handbook from our 2015 Bioinformatics Workshop for Helminth Genomics:
The ‘Variome’ section of the handbook from our 2015 Bioinformatics Workshop for Helminth Genomics:
We’ve developed a protocol for annotating kinase domains in nematodes and platyhelminthes and published the method on the Nature Protocol Exchange:
We’ve published our protocols for genomic and transcriptomic data production, assembly and quality control on the Nature Protocol Exchange:
We published our method for defining sets of core genes for nematodes, trematodes and cestodes for use in training gene predictors in the Nature Protocol Exchange:
Finding set of “core genes” for Nematoda, Trematoda and Cestoda
We’ve published a method for the characterizing and comparing the metabolic potential of worm parasites in the Nature Protocol Exchange:
In collaboration with Dr. John Parkinson’s lab we’ve developed a protocol for annotating metabolic enzymes in parasitic worms