Pinned Repositories
fungorum
R package to access records from Index Fungorum
FUNGuildR
Look Up Guild Information for Fungi in R
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
optimotu.pipeline
R pipeline for environmental DNA barcoding
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/phylotax
Refine taxonomic assignments of environmental sequences using a phylogenetic tree
brendanf/ShortRead
Fork of ShortRead from Bioconductor which skips checking for zlib during installation.
brendanf/tzara
Cluster long amplicons using dada2 denoising on variable regions
brendanf/brendan
Short utility functions
brendanf/brms
brms R package for Bayesian generalized multivariate non-linear multilevel models using Stan
brendanf/clustermq
R package to send function calls as jobs on LSF, SGE, Slurm, PBS/Torque, or each via SSH
brendanf/conda_r_skeleton_helper
Cleaning up Conda r-packages
brendanf/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
brendanf/drake
An R-focused pipeline toolkit for reproducibility and high-performance computing
brendanf/FUNGuild
FUNGuild: parsing OTUs into functional guilds
brendanf/gefast
Generalised Fastidious Swarming Tool
brendanf/ggtree
:christmas_tree:Visualization and annotation of phylogenetic trees
brendanf/ips
R Interfaces to Phylogenetic Software
brendanf/mptp
mPTP - a tool for single-locus species delimitation
brendanf/odseq
Outlier detection in multiple sequence alignment
brendanf/packrat
Packrat is a dependency management system for R
brendanf/r-drake-feedstock
A conda-smithy repository for r-drake.
brendanf/r-fst-feedstock
A conda-smithy repository for r-fst.
brendanf/r-ips-feedstock
A conda-smithy repository for r-ips.
brendanf/r-qdap-feedstock
A conda-smithy repository for r-qdap.
brendanf/r-targets-feedstock
A conda-smithy repository for r-targets.
brendanf/slurm
Cookiecutter for snakemake slurm profile
brendanf/snakecharm
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
brendanf/sysreqsdb
SystemRequirements mappings for R packages
brendanf/tensorflow-feedstock
A conda-smithy repository for tensorflow.
brendanf/vegan
R package for community ecologists: popular ordination methods, ecological null models & diversity analysis
brendanf/XStringSetViews
Store Multiple Views on an XStringSet