Mercurial > repos > kpbioteam > ewastools

annotate README.md @ 81:8ab24a5229bd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
author kpbioteam
date Tue, 11 Feb 2020 09:14:55 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
81
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
1 [![Build Status](https://travis-ci.org/kpbioteam/ewas_galaxy.svg?branch=master)](https://travis-ci.org/kpbioteam/ewas_galaxy)
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
2
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
3
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
4 # 🔬📚 Infinium Human Methylation BeadChip: a pipeline for population epigenetics integrated into Galaxy
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
5
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
6 This repository contains Infinium Human Methylation BeadChip pipeline that can be installed and used inside the Galaxy.
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
7 The Tool is avaliable through [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu/view/kpbioteam/ewastools/53aaf097238c) and ready to use via [Docker](https://galaxyproject.org/use/ewas-galaxy/).
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
8
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
9 Analysis pipline includes:
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
10 * raw intensity data loading
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
11 * .idat preprocessing
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
12 * optional normalisation of the data and quality control with additional sample check.
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
13
8ab24a5229bd "planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed"
kpbioteam
parents:
diff changeset
14 This gives the user the opportunity to perform any of these preparation and data cleaning steps, including a recommended 'genetic variation annotation step'. Finally, the generated dataset can be used to hunt (find) differentially-methylated positions DMP and regions DMR with respect to a phenotype co-variate.