ccdmb repositories

27 repositories

EffectorFisher-core
Public
🧬 EffectorFisher links pangenome isoforms to disease traits to predict phenotype-associated effectors. 🌾🦠
Python
•
MIT License
•0•0•0•0•Updated Jul 8, 2026Jul 8, 2026
EFtranslocator
Public
Predict various features relevant to plant host-cell translocation and sub-cellular localisation, for a given protein FASTA input
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 1, 2026Jul 1, 2026
SUSSscan
Public
Scan fungal proteome FASTA for identifiable effectors and predicted SUSS structural families based on RemEff clusters
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 1, 2026Jul 1, 2026
predector
Public
Effector prediction pipeline based on protein properties.
Shell
•
Apache License 2.0
•10•17•15•1•Updated Jul 18, 2025Jul 18, 2025
predector-utils
Public
Utilities for running the predector pipeline.
Python
•
Apache License 2.0
•1•0•2•1•Updated Apr 11, 2025Apr 11, 2025
postasm
Public
QC and tidying on assembled genomes.
bioinformatics quality-control pipeline
bioinformatics quality-control pipeline genomics bioinformatics-pipeline genome-assembly genome-assembly-evaluation
Groovy
•
Apache License 2.0
•1•0•0•0•Updated Nov 15, 2024Nov 15, 2024
pante
Public
A pipeline for predicting and masking transposable elements in multiple genomes.
Groovy
•
Apache License 2.0
•10•0•0•0•Updated Nov 15, 2024Nov 15, 2024
qcflow
Public
Perform basic QC on illumina data
bioinformatics quality-control pipeline
bioinformatics quality-control pipeline genomics bioinformatics-pipeline illumina fastq
Groovy
•
MIT License
•1•0•0•0•Updated Nov 15, 2024Nov 15, 2024
mitoflow
Public
A small pipeline for assembling mitochondrial genomes and filtering reads prior to assembly.
bioinformatics pipeline genomics
bioinformatics pipeline genomics assembly bioinformatics-pipeline genome-assembly mitochondria
Groovy
•
MIT License
•1•0•0•0•Updated Nov 15, 2024Nov 15, 2024
ccdmb.github.io
Public
Front page for the CCDM bioinformatics group.
Apache License 2.0
•0•0•0•0•Updated Nov 13, 2023Nov 13, 2023
nanopore_assembly
Public
Nextflow
•0•0•0•0•Updated May 10, 2023May 10, 2023
barley-DH-pow-rnaseq
Public
RNA-seq analysis of barley double haploid (DH) lines from Baudin / Eth069 cross during powdery mildew disease
MIT License
•0•0•0•0•Updated May 2, 2023May 2, 2023
R_Script_templates
Public
Example templates for bioinformatics analyses
rstudio
rstudio
HTML
•0•0•0•0•Updated Apr 18, 2023Apr 18, 2023
catastrophy
Public
CATAStrophy predicts filamentous plant pathogen lifestyle characteristics based on their CAZyme composition.
bioinformatics pathogen fungi
bioinformatics pathogen fungi trophic-interactions pathogenomics
Python
•
BSD 3-Clause "New" or "Revised" License
•0•6•2•0•Updated Jan 16, 2023Jan 16, 2023
wheat-agr-tanspot
Public
RNA-seq analysis of wheat AGR during tan spot infection
MIT License
•0•0•0•0•Updated Dec 9, 2022Dec 9, 2022
slurm_scripts
Public
SLURM script collection
Shell
•1•1•0•0•Updated Nov 21, 2022Nov 21, 2022
PTR-60
Public
PTR gene analysis for race 2 and 4 isolates PacBio sequenced
MIT License
•0•0•0•0•Updated Jun 15, 2022Jun 15, 2022
catastrophy-pipeline
Public archive
Easily run the CATAStrophy classifier on many genomes.
Nextflow
•
Apache License 2.0
•0•1•0•0•Updated Oct 2, 2021Oct 2, 2021
predector-data
Public
Datasets used for developing the predector pipeline
Jupyter Notebook
•0•0•0•0•Updated Aug 20, 2021Aug 20, 2021
BioDendro
Public
A package to cluster and visualise MS/MS spectral data
clustering metabolomics analytes
clustering metabolomics analytes plot-dendrograms
Jupyter Notebook
•
Apache License 2.0
•1•11•0•0•Updated Feb 26, 2021Feb 26, 2021
barley-pow-rnaseq
Public
Barley Baudin and Palace NIL RNAseq analysis during powdery mildew infection
Apache License 2.0
•0•1•0•0•Updated Aug 17, 2020Aug 17, 2020
20200306-pnodorum_pangenome_pseudocode
Public
Code accompanying an upcoming manuscript on a P. nodorum pangenome.
Shell
•
Apache License 2.0
•0•0•0•0•Updated Jun 16, 2020Jun 16, 2020
PathoPore
Public
PathoPore - Longer Sequences and NextFlow Faster Analysis
nanopore pathogens nextflow-pipeline
nanopore pathogens nextflow-pipeline
Nextflow
•
Apache License 2.0
•1•0•0•0•Updated Nov 14, 2019Nov 14, 2019
mumflow
Public
A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
bioinformatics pipeline genomics
bioinformatics pipeline genomics bioinformatics-pipeline alignment pangenomics
Python
•
Apache License 2.0
•3•0•0•0•Updated Sep 24, 2019Sep 24, 2019
snptree
Public
A nextflow pipeline to run phylogenetic analyses using SNPs
bioinformatics snps pipeline
bioinformatics snps pipeline genomics bioinformatics-pipeline phylogenetics
Nextflow
•
Apache License 2.0
•1•0•0•0•Updated May 15, 2019May 15, 2019
pclust
Public
A nextflow pipeline to cluster sets of proteins.
bioinformatics pipeline protein
bioinformatics pipeline protein bioinformatics-pipeline effector protein-clustering protein-function-prediction
Groovy
•
MIT License
•1•0•0•0•Updated Apr 24, 2019Apr 24, 2019
panann
Public
Pipelines for gene and TE annotation of pangenomes.
pipeline genomics genome-annotation
pipeline genomics genome-annotation gene-prediction
Dockerfile
•
Apache License 2.0
•2•0•0•0•Updated Apr 23, 2019Apr 23, 2019

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CCDM Bioinformatics

All

27 repositories

EffectorFisher-core

EFtranslocator

SUSSscan

predector

predector-utils

postasm

pante

qcflow

mitoflow

ccdmb.github.io

nanopore_assembly

barley-DH-pow-rnaseq

R_Script_templates

catastrophy

wheat-agr-tanspot

slurm_scripts

PTR-60

catastrophy-pipeline

predector-data

BioDendro

barley-pow-rnaseq

20200306-pnodorum_pangenome_pseudocode

PathoPore

mumflow

snptree

pclust

panann

Repositories list

27 repositories