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Name: Science For Life Laboratory

Type: Organization

Bio: Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research

Location: Stockholm University

Blog: http://www.scilifelab.se

Scilifelab modules

Installation

Installation is as simple as

python setup.py install

If you are running several virtual environments, where one (e.g. devel) is used for development, you can install a development version by running

workon devel
python setup.py develop

Documentation

Docs are located in the doc directory. To install, cd to doc and run

make html

Documentation output is found in build.

Running the tests

The modules are shipped with a number of unit tests, located in the tests directory. To run a test, issue the command

python setup.py nosetests

or if you want to run individual tests, cd to tests and run (for example)

nosetests -v -s test_db.py

Science For Life Laboratory's Projects

bcbb

Useful bioinformatics code, primarily in Python and R

bcbio-nextgen

Best-practice pipelines for fully automated high throughput sequencing analysis

bcbio-nextgen-deploy

Suite of scripts to automatically deploy nextgen pipeline

bravo-protocols

VWorks protocols and other files for the Agilent NGS Workstations at the Genomics facility at SciLifeLab.

caw-containers

Containers for CAW

cloudbiolinux

CloudBioLinux: automating resource preparation for biological analysis

coronastatus

Open source webapp that let people report their health status to get overview of COVID-19 🇳🇴🇳🇱🇸🇰🇲🇽🇮🇹🇮🇳🇵🇭🇸🇪🇩🇰🇹🇷🇧🇪

courses

Course homepages for some of the courses given at SciLifeLab

dotfiles

external_kpis

facs

Fast and Accurate Classification of Sequences using Bloom filters

flowcell_parser

Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output

gapest

Reference implementation of the scaffolding gap size estimation algorithm by Kristoffer Sahlin

genologics

Python interface to the GenoLogics LIMS server via its REST API.

genologics_sql

Python interface for the Genologics Postgres database.

genomics-dashboard

genomics-status

Tornado server for tracking samples at NGI Stockholm

hugin

Status monitor

internal-provisioning

Ansible repository for deployment stuff

joint_variant_calling

lims2db

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/)

ngi-cellraiser

Pipeline for analysing 10X single cell data

ngi-chipseq

Nextflow ChIP-seq data analysis pipeline, National Genomics Infrastructure, Science for Life Laboratory in Stockholm

ngi-exoseq

This pipeline has moved! Please see:

ngi-methylseq

This pipeline has moved! Please see:

ngi-neutronstar

De novo assembly pipeline for 10X linked-reads, used at the SciLifeLab National Genomics Infrastructure.

ngi-nextflowdocs

Common documentation for National Genomics Infrastructure pipelines built with Nextflow

ngi-rnafusion

RNA pipeline for fusion detection

scilifelab Goto Github PK

Scilifelab modules

Installation

Documentation

Running the tests

Science For Life Laboratory's Projects

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