Pinned Repositories
catastrophy
CATAStrophy predicts filamentous plant pathogen lifestyle characteristics based on their CAZyme composition.
predector
Effector prediction pipeline based on protein properties.
fungraph
Prototype pipeline for fungal pangenome graphs.
gffpal
A flexible library for working with GFF data.
gi-to-tax
Finds taxonomic information for a given set of genbank identifiers, using the NCBI taxonomy database.
mitoflow
A small pipeline for assembling mitochondrial genomes and filtering reads prior to assembly.
mumflow
A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
panann
Pipelines for gene annotation of pangenomes.
pante
A pipeline for predicting and masking transposable elements in multiple genomes.
darcyabjones's Repositories
darcyabjones/panann
Pipelines for gene annotation of pangenomes.
darcyabjones/pante
A pipeline for predicting and masking transposable elements in multiple genomes.
darcyabjones/gffpal
A flexible library for working with GFF data.
darcyabjones/selectml
A package for performing and optimising genomic selection using machine learning
darcyabjones/ffdb
Script for manipulating ffindex databases
darcyabjones/GenoClustR
An R package for finding genomic clusters of co-regulated genes
darcyabjones/INFEST
Python script to compute kinematics of lesion development
darcyabjones/riprap
Tools for detecting and quantifying RIP-like signatures in genomes.
darcyabjones/20230424-sclerotinia_transcriptomics_metaanalysis
Repository containing code used to analyse Sclerotinia transcriptomics data
darcyabjones/ApoplastP
Prediction of effectors and plant proteins in the plant apoplast using machine learning
darcyabjones/bash_utils
Functions to make bash go nice
darcyabjones/bioscripts
Handy scripts to use
darcyabjones/darcyabjones.github.io
darcyabjones/deepredeff-py
A python port of the deepredeff R-package
darcyabjones/deepsig
DeepSig - Predictor of signal peptides in proteins based on deep learning
darcyabjones/dotfiles
My configs and dotfiles for the terminal
darcyabjones/EffectorP-1.0
EffectorP: predicting fungal effector proteins from secretomes using machine learning
darcyabjones/EffectorP-2.0
Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0
darcyabjones/EffectorP-3.0
Prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes
darcyabjones/ggff
A gff manipulation tool
darcyabjones/gperceiver
Perceiver neural network building blocks
darcyabjones/how_are_we_stranded_here
Check strandedness of RNA-Seq fastq files
darcyabjones/jb2_nginx_passwd
darcyabjones/jbrowse2-nocompile-plugins
Some helper functions for customising JBrowse2 servers
darcyabjones/LOCALIZER
LOCALIZER: subcellular localization prediction of plant and effector proteins in the plant cell
darcyabjones/pafplot
Plot genome alignment dot plots quickly
darcyabjones/prj
A simple, opiniated, data analysis backup and change logging utility.
darcyabjones/rocker_extended
Utilities and extended definition files for Rstudio rocker containers.
darcyabjones/slurm_scripts
SLURM script collection
darcyabjones/windowstackr
An HTML widget to have a desktop window-like interface in R-shiny apps.