Pinned Repositories
jgi-query
A simple command-line tool to download data from Joint Genome Institute databases
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
Agaricomycetes_species_distribution_adjustment
This code was used in Varga et al. 2019 (https://www.nature.com/articles/s41559-019-0834-1#Sec4): "We adjusted taxon sampling in our phylogeny by iteratively deleting species from genera that were oversampled relative to the mean sampling fraction of the tree, until sampling fractions of each genera corresponded their known size as judged by a comparison to Species Fungorum. To do this, we performed a hypergeometric test (P < 0.05) at each iteration of species removal. Elimination of species was stopped when oversampling disappeared (P > 0.05, hypergeometric test)."
CompareTools
R package to analyse the output of compare program
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
PhyloGenie
A pipeline to download, tidy up publicly available sequences, generate phylogenies and more
StatesThroughTimePlot
An R code used for plotting inferred ancestral states through time in this article: https://www.nature.com/articles/s41559-019-0834-1
tgexer
Tissue-specific gene expression examiner
TraitEvolution
Some R functions for analyze the output of ancestral state reconstruction (ASR) analyses
TransformNewickSupport
An R script which transforms a newick treefile structure to be acceptable for the Notung program
vtorda's Repositories
vtorda/Agaricomycetes_species_distribution_adjustment
This code was used in Varga et al. 2019 (https://www.nature.com/articles/s41559-019-0834-1#Sec4): "We adjusted taxon sampling in our phylogeny by iteratively deleting species from genera that were oversampled relative to the mean sampling fraction of the tree, until sampling fractions of each genera corresponded their known size as judged by a comparison to Species Fungorum. To do this, we performed a hypergeometric test (P < 0.05) at each iteration of species removal. Elimination of species was stopped when oversampling disappeared (P > 0.05, hypergeometric test)."
vtorda/CompareTools
R package to analyse the output of compare program
vtorda/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
vtorda/PhyloGenie
A pipeline to download, tidy up publicly available sequences, generate phylogenies and more
vtorda/StatesThroughTimePlot
An R code used for plotting inferred ancestral states through time in this article: https://www.nature.com/articles/s41559-019-0834-1
vtorda/tgexer
Tissue-specific gene expression examiner
vtorda/TraitEvolution
Some R functions for analyze the output of ancestral state reconstruction (ASR) analyses
vtorda/TransformNewickSupport
An R script which transforms a newick treefile structure to be acceptable for the Notung program