Kimberly Coetzer's starred repositories
py2cytoscape
Python utilities for Cytoscape and Cytoscape.js
open-cravat
A modular annotation tool for genomic variants
py4cytoscape
Python library for calling Cytoscape Automation via CyREST
ProteomicsVisualization
This is a collection of minimal code to visualize various aspects of proteomics data.
msproteomicstools
Some hopefully useful tools for mass spectrometry applied to proteomics
bamtofastq
Converts bam or cram files to fastq format and does quality control.
containers-rules-manuscript
Recommendations to contenarized your bioinformatics software
proteogenomics_python
python scripts for proteogenomics analysis
SpliceVista
Splice variant analysis in shotgun proteomics data
MAXOMOD_Pipeline
Reproducible analysis pipeline for the MAXOMOD project: Multiomic ALS signatures highlight sex differences and molecular subclusters and identify the MAPK pathway as therapeutic target
fetchngs2rnaseq
Meta-pipeline for nf-core/fetchngs -> nf-core/rnaseq
quantms-utils
A python library with scripts and helpers classes for quantms workflow
omicsgenetraitassociation
A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis
multi-package-containers
Testing building mulled containers for multi-requirement tools.
test_nfcore_workflow_chain
This is now outdated as the template has changed dramatically.
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
ppi_validation_process
Python pipelines to filter positive predicted protein interactions according to two criteria: (i) association rules of cellular components according to gold standard PPI data from HINT and (ii) text mining on scientific papers published on Pubmed extracting sentences where the proteins in the PPIs appeared in an interaction context
cluster-analysis
A set of R scripts to analyse the data from PRIDE Cluster
dockerfiles
This repository holds Dockerfiles for creating docker images for several OpenMS configurations based on different base images.
proteogenomics-analysis-workflow
IPAW: a Nextflow workflow for proteogenomics
proteogenomics_python
python scripts for proteogenomics analysis