Pinned Repositories
bioconda-recipes
Conda recipes for the bioconda channel.
blend4j
blend4j is a JVM partial reimplemenation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.
cistrome_beta
Distributions from http://cistrome.org/BETA/
compomics-utilities
Open-source java library for computational proteomics
cufflinks
download_store
Universal storage for tarballs and binaries that are not guaranteed to exist for a long time. This reposititory is mainly used to enable reproducibility within Galaxy and the Galaxy Tool Shed.
eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
galaxytools
Galaxy Tool wrappers
mztosqlite
Convert proteomics data files into a SQLite database
ontology_lookup_client
Client application to retrieve entries from the EBI ontology web service.
jj-umn's Repositories
jj-umn/galaxytools
Galaxy Tool wrappers
jj-umn/mztosqlite
Convert proteomics data files into a SQLite database
jj-umn/bioconda-recipes
Conda recipes for the bioconda channel.
jj-umn/cistrome_beta
Distributions from http://cistrome.org/BETA/
jj-umn/compomics-utilities
Open-source java library for computational proteomics
jj-umn/cufflinks
jj-umn/download_store
Universal storage for tarballs and binaries that are not guaranteed to exist for a long time. This reposititory is mainly used to enable reproducibility within Galaxy and the Galaxy Tool Shed.
jj-umn/eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
jj-umn/FragPipe
A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
jj-umn/galaxy
Data intensive science for everyone.
jj-umn/galaxytools-1
:microscope::books: Galaxy Tool wrappers
jj-umn/galaxytools-2
jj-umn/graph2pro-var
jj-umn/mayu
Mayu - Protein Identification False Discovery Rates
jj-umn/metaquantome
jj-umn/Morpheus
Morpheus mass spectrometry–based proteomics database search algorithm
jj-umn/optitype_venv
Prebuilt OptiType python virtual environment fo Linux
jj-umn/peptide-shaker
Interpretation of proteomics identification results
jj-umn/proBAMconvert
proBAMconvert, a conversion tool for peptide identification files (MzIdentML,pepXML,mzTAB) to the proBAM format
jj-umn/prosit
Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. When using Prosit is helpful for your research, please cite "Gessulat, Schmidt et al. 2019" DOI 10.1038/s41592-019-0426-7
jj-umn/psm-eval
Python application and framework for reanalyzing peptide-spectrum-matches (PSMs).
jj-umn/ScanNeo
A pipeline for identifying indel derived neoantigens using RNA-Seq data
jj-umn/TINT
jj-umn/tools-devteam
Repository encapsulating a set of Galaxy tools mostly written by the Galaxy Team.
jj-umn/tools-galaxyp
Galaxy Tool Shed repositories maintained and developed by the GalaxyP community
jj-umn/tools-iuc
Tool Shed repositories maintained by the Intergalactic Utilities Commission
jj-umn/training-material
A collection of Galaxy-related training material
jj-umn/transIndel
Indel caller for DNA-seq or RNA-seq
jj-umn/twobitreader
A fast python class for reading 2-bit files (used by UCSC genome browser)
jj-umn/usegalaxy-eu-tools
List of tools included in https://usegalaxy.eu