darcyabjones

panann

Pipelines for gene annotation of pangenomes.

pante

A pipeline for predicting and masking transposable elements in multiple genomes.

gffpal

A flexible library for working with GFF data.

selectml

A package for performing and optimising genomic selection using machine learning

ffdb

Script for manipulating ffindex databases

GenoClustR

An R package for finding genomic clusters of co-regulated genes

INFEST

Python script to compute kinematics of lesion development

riprap

Tools for detecting and quantifying RIP-like signatures in genomes.

20230424-sclerotinia_transcriptomics_metaanalysis

Repository containing code used to analyse Sclerotinia transcriptomics data

ApoplastP

Prediction of effectors and plant proteins in the plant apoplast using machine learning

bash_utils

Functions to make bash go nice

be_loc

A thin CLI wrapper around the bioembeddings feature extraction tools.

bioscripts

Handy scripts to use

deepredeff-py

A python port of the deepredeff R-package

deepsig

DeepSig - Predictor of signal peptides in proteins based on deep learning

dotfiles

My configs and dotfiles for the terminal

EffectorP-1.0

EffectorP: predicting fungal effector proteins from secretomes using machine learning

EffectorP-2.0

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

EffectorP-3.0

Prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes

ggff

A gff manipulation tool

gperceiver

Perceiver neural network building blocks

how_are_we_stranded_here

Check strandedness of RNA-Seq fastq files

jb2_nginx_passwd

jbrowse2-nocompile-plugins

Some helper functions for customising JBrowse2 servers

LOCALIZER

LOCALIZER: subcellular localization prediction of plant and effector proteins in the plant cell

pafplot

Plot genome alignment dot plots quickly

prj

A simple, opiniated, data analysis backup and change logging utility.

profiles

My zsh, bash, tmux and vim profiles.

rocker_extended

Utilities and extended definition files for Rstudio rocker containers.

slurm_scripts

SLURM script collection