jj-umn Goto Github PK

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

fragpipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data

galaxy

Data intensive science for everyone.

galaxy-central

git repo tracking galaxy-central's mercurial repository (https://bitbucket.org/galaxy/galaxy-central)

galaxytools

Galaxy Tool wrappers

galaxytools-1

:microscope::books: Galaxy Tool wrappers

galaxytools-2

graph2pro-var

mayu

Mayu - Protein Identification False Discovery Rates

metaquantome

morpheus

Morpheus mass spectrometry–based proteomics database search algorithm

mztosqlite

Convert proteomics data files into a SQLite database

ontology_lookup_client

Client application to retrieve entries from the EBI ontology web service.

optitype_venv

Prebuilt OptiType python virtual environment fo Linux

peptide-shaker

Interpretation of proteomics identification results

probamconvert

proBAMconvert, a conversion tool for peptide identification files (MzIdentML,pepXML,mzTAB) to the proBAM format

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

psm-eval

Python application and framework for reanalyzing peptide-spectrum-matches (PSMs).

scanneo

A pipeline for identifying indel derived neoantigens using RNA-Seq data

tint

tools-devteam

Repository encapsulating a set of Galaxy tools mostly written by the Galaxy Team.

tools-galaxyp

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community

tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission

training-material

A collection of Galaxy-related training material