Pinned Repositories
fungorum
R package to access records from Index Fungorum
FUNGuildR
Look Up Guild Information for Fungi in R
GSSP
Global Spore Sampling Project
inferrnal
R Interface to Call Programs from Infernal RNA Covariance Model Package
LSUx
Cut rDNA sequences into domains using covariance models
optimotu
Optimize OTU clustering thresholds
phylotax
Refine taxonomic assignments of environmental sequences using a phylogenetic tree
reUnite
Reannotate RDP, Warcup, and Unite databases to use uniform taxonomic classifications
rITSx
Extract ITS and Neighboring Regions from Eukaryotic DNA Sequences
tzara
Cluster long amplicons using dada2 denoising on variable regions
brendanf's Repositories
brendanf/FUNGuildR
Look Up Guild Information for Fungi in R
brendanf/inferrnal
R Interface to Call Programs from Infernal RNA Covariance Model Package
brendanf/optimotu
Optimize OTU clustering thresholds
brendanf/reUnite
Reannotate RDP, Warcup, and Unite databases to use uniform taxonomic classifications
brendanf/rITSx
Extract ITS and Neighboring Regions from Eukaryotic DNA Sequences
brendanf/fungorum
R package to access records from Index Fungorum
brendanf/GSSP
Global Spore Sampling Project
brendanf/LSUx
Cut rDNA sequences into domains using covariance models
brendanf/optimotu.pipeline
R pipeline for environmental DNA barcoding
brendanf/unite_cluster_optimization
Optimize single-linkage clustering thresholds for barcoding genes to approximate known taxonomic annotations
brendanf/bioconda-recipes
Conda recipes for the bioconda channel.
brendanf/bistorta_vivipara_translocation
Bioinformatics pipeline for "Experimental evidence on the influence of root-associated fungi on plant growth along altitude"
brendanf/CORAL_bioinfo
Bioinformatics pipeline for data used in CORAL paper
brendanf/crew.cluster
crew launcher plugins for traditional high-performance computing clusters
brendanf/deadwood_priority_effects
Bioinformatics pipeline for "Idiosyncratic responses to biotic and environmental filters in wood-inhabiting fungal communities"
brendanf/deadwood_restoration
Bioinformatics pipeline for 'Natural deadwood hosts more diverse pioneering wood-inhabiting fungal communities than restored deadwood'
brendanf/edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
brendanf/nng-feedstock
A conda-smithy repository for nng.
brendanf/PifCoSm
Pipeline for Construction of Supermatrices
brendanf/protaxA
PROTAX for aligned sequences
brendanf/r-igraph-feedstock
A conda-smithy repository for r-igraph.
brendanf/r-nanonext-feedstock
A conda-smithy repository for r-nanonext.
brendanf/RogueNaRok
A versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index
brendanf/sh_matching_pub
brendanf/SneakySnake
SneakySnake is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al.
brendanf/spoar
SIMD Partial Order Alignment in R
brendanf/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
brendanf/targets
Function-oriented Make-like declarative workflows for R
brendanf/tidytree
:shower:A Tidy Tool for Phylogenetic Tree Data Manipulation
brendanf/WFA2-lib
WFA2-lib: Wavefront alignment algorithm library v2