multiscale-genomics Goto Github PK

atac-seq

bam_qc

Wrapper for BamQC

chi-c

dnaflexbrowser

The DNA Flex Browser lets you navigate through sequence-dependent DNA flexibility data.

dnaflexsuite

A suite of tools to predict DNA flexibility from sequence at different resolutions

ftdock

Rigid-body protein-DNA sampling

mg-common

Common functions that are not specific to a given workflow or tool

mg-dm-api

API for the management of file locations and users within the MuG VRE

mg-docs

Documentation for developers creating tools and pipelines for the MuG VRE

mg-misc-scripts

Miscellaneous scripts for mg-process-fastq

mg-process-benchmark

Wrappers around mg Tools that have been written in Luigi so that they can be run on alternative cluster technologies to aid in benchmarking the pipelines

mg-process-fastq

Scripts required for the processing of FASTQ files (eg generating adjacency lists for Hi-C data)

mg-process-files

Scripts for processing bed, wig and tsv files ready for indexing for the RESTful servers.

mg-process-macs2

Pipeline wrapping the MACS2 tool for the MuG Tool Developers API Workshop

mg-process-test

Example pipelines file that is ready to run in the VRE matching the code in the HowTo documentation

mg-rest-3d

RESTful API for TADbit generated 3D coordinates

mg-rest-adjacency

RESTful API providing adjacency data stored in hdf5 files that have been generated with the scripts in the mg-storage-hdf5 / mg-process-fastq repo

mg-rest-dm

RESTful access to the DMP

mg-rest-file

Data retrieval of files or sections of files

mg-rest-ge

REST API for gene expression data generated as part of teh MuG project.

mg-rest-mysql

RESTful API to an adjacency matrix stored in a MySQL db

mg-rest-service

Service to monitor REST live services

mg-rest-tad

RESTful API to TAD predictions

mg-rest-util

Util functions common to all rest services

mg-storage-hdf5

Repository for code related to the storage of adjacency matrix data in the HDF5 file format

mg-tool-api

This library outlines the main structures related to the tools section of the VRE.

mugin

The MuG Information Network visualises information flow in Multiscale Complex Genomics.

multiscale-genomics.github.io

Github.io Jekyll site for the Multiscal Genomics repository

pychic

Repository containing pipeline and tools to analyse capture Hi-C data

pydockdna_tool

VRE pyDockDNA tool manager