Phil Ewels

Login: ewels

Company: Science for Life Laboratory

Location: Stockholm, Sweden

Bio: Bioinformatician working with next generation sequencing data.

Blog: http://phil.ewels.co.uk

Blog: http://phil.ewels.co.uk

Member of

1. MultiQC
2. National Genomics Infrastructure
3. nf-core
4. Science For Life Laboratory

Repositories

10XQC

A system for monitoring the quality of 10X single cell data

airbnb-beautifier

Userscript that makes Airbnb search results' map bigger

awesome-10x-genomics

List of tools and resources related to the 10x genomics GEMCode/Chromium system

AWS-iGenomes

Documentation and description of AWS iGenomes S3 resource.

BamQC

Mapped QC analysis program

bioconda-recipes

Conda recipes for the bioconda channel.

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bootstrap-feature-widgets

A simple widget which makes markup for a feature using Twitter Bootstrap styles

ClusterFlow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

clusterflow-uppmax

UPPMAX specific scripts and resources for Cluster Flow

clusterflow-website

Files that power the Cluster Flow website: http://clusterflow.io

colormath-feedstock

A conda-smithy repository for colormath.

CPT-Bootstrap-Carousel

WordPress plugin which generates a custom post type for choosing images and content. Outputs Bootstrap Image Carousel (slider) HTML from a shortcode.

film-finder-db

Film Finder Database

genomics-status

Files used to run the genomics status website at SciLifeLab

hack17

Nextflow hackathon 2017 projects

hemnet-commuter

Given an RSS feed of a Hemnet search, filter for properties that match a commuting preference.

irma-provision

Ansible playbooks for provisioning NGI pipeline and related sw

jobstats-explorer

Dump job metadata from UPPMAX, then explore it in a web front-end.

Labrador

A web based tool to manage and automate the processing of publicly available datasets.

leeHom

Bayesian reconstruction of ancient DNA fragments

lz-string-python

lz-string for python 2/3

MegaQC

Web application to collect and visualise data across multiple MultiQC runs.

MegaQC_website

Website files for MegaQC. See https://github.com/ewels/MegaQC

miRNA_processing

Scripts to process miRNA from trimming through annotation.

modules.sf.net

Adhoc software "packaged" for the ancient and deprecated "module system" (http://modules.sf.net/)

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

MultiQC_Clarity

MultiQC plugin interacting with the Illumina Genologics Clarity LIMS

MultiQC_NGI

MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.

MultiQC_OSXApp

Files and config for OS X wrapper around MultiQC. See https://github.com/ewels/MultiQC

MultiQC_TestData

Test data for MultiQC. See https://github.com/ewels/MultiQC

MultiQC_website

Website files for MultiQC. See https://github.com/ewels/MultiQC

nextflow

A DSL for data-driven computational pipelines

nf-co.re

See the main fork of this repository here >>>

nf-core-chipseq

See the main fork of this repository here >>>

nf-core-chipseq

See the main fork of this repository here >>>

NGI-NFcookiecutter

Template for your own top-end Nextflow pipeline, customised using Cookiecutter

NGI-NFcookiecutter

Template for your own top-end Nextflow pipeline, customised using Cookiecutter

nf-core-exoseq

See the main fork of this repository here >>>

nf-core-exoseq

See the main fork of this repository here >>>

nf-core.github.io

Documentation website for the nf-core community

nf-core-logos

See the main fork of this repository here >>>

NGI-MethylSeq

Methylation (Bisulfite-Sequencing) analysis pipeline used at SciLifeLab NGI. Main fork:

NGI-MethylSeq

Methylation (Bisulfite-Sequencing) analysis pipeline used at SciLifeLab NGI. Main fork:

nf-core-RNAseq

See the main fork of this repository here >>>

nf-core-RNAseq

See the main fork of this repository here >>>

nf-core-RNAseq

See the main fork of this repository here >>>

nf-core-RNAseq

See the main fork of this repository here >>>

nf-core-RNAseq

See the main fork of this repository here >>>

nf-core-RNAseq

See the main fork of this repository here >>>

nf-core-test-datasets

See the main fork of this repository here >>>

nf-core-tools

See the main fork of this repository here >>>

nf-core-chipseq

See the main fork of this repository here >>>

nf-core-chipseq

See the main fork of this repository here >>>

NGI_dashboards

SciLifeLab NGI Dashboard Code

nf-core-exoseq

See the main fork of this repository here >>>

nf-core-exoseq

See the main fork of this repository here >>>

NGI-MethylSeq

Methylation (Bisulfite-Sequencing) analysis pipeline used at SciLifeLab NGI. Main fork:

NGI-MethylSeq

Methylation (Bisulfite-Sequencing) analysis pipeline used at SciLifeLab NGI. Main fork:

NGI-NeutronStar

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NGI-NextflowDocs

Common documentation for National Genomics Infrastructure pipelines built with Nextflow

NGI-NFcookiecutter

Template for your own top-end Nextflow pipeline, customised using Cookiecutter

NGI-NFcookiecutter

Template for your own top-end Nextflow pipeline, customised using Cookiecutter

ngi_reports

Code to generate reports for use by the NGI in SciLifeLab

NGI-RNAfusion

Attempt at setting up a pipeline for fusion detection as an addon to the previously existing NGI-RNAseq pipeline.

nf-core-RNAseq

See the main fork of this repository here >>>

nf-core-RNAseq

See the main fork of this repository here >>>

nf-core-RNAseq

See the main fork of this repository here >>>

NGI-smRNAseq

Nextflow Small RNA Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

ngi_visualizations

Next-Gen Sequencing Visualisation Scripts.

niceLiftOver

Wrapper script to take an input file and liftOver the co-ordinates in place, leaving all other data in tact.

opensource.scilifelab-theme

WordPress theme for Open Source SciLifeLab website.

OrderPortal

A portal for orders (= requests, project applications) for one or more facilities.

phil.ewels.co.uk

Website code for phil.ewels.co.uk

pm

Project and Data management for NGI Sweden

python-colormath

A python module that abstracts common color math operations. For example, converting from CIE L*a*b to XYZ, or from RGB to CMYK

RepEnrich

RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.

Sarek

Sarek: a complete open source pipeline to detect germline, or somatic variants from WGS data

scilifelab

Misc code snippets for Science For Life Laboratory

SeqMonk

SeqMonk NGS visualisation and analysis tool

sequences

A lightweight and quick DNA sequence manipulation tool.

spectra-feedstock

A conda-smithy repository for spectra.

sra-explorer

Web application to explore the Sequence Read Archive.

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

standalone_scripts

Repository to store standalone scripts that do not belong to any bigger package or repository

statusdb

Python wrappers and methods to work with CouchDB's instance at NGI Stockholm

tallphil.co.uk

Jekyll blog for tallphil.co.uk

thesis

null

tldr

:books: Simplified and community-driven man pages

tldr-bash

Simplified and community-driven man pages http://tldr-pages.github.io/

TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

WP-OAuth

A WordPress plugin that allows users to login or register by authenticating with an existing Google, Facebook, LinkedIn, Github, Reddit or Windows Live account via OAuth 2.0. Easily drops into new or existing sites, integrates with existing users.

www.htslib.org

The htslib.org web site

Commits To