Hammarn

1MB335

Repository for developing the new labs for 1MB335

NGI-RNAfusion

Old initial repo of the pipeline, main repo here:

Populationsgenomik

Repo for the lab in the courses 1BG508 and 1BG512

NGI-smRNAseq

AdmixTools

Tools test whether admixture occurred and more

Dockerfiles

A collection of dockerfiles I've made of software

flowcell_parser

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

genomics-status

Tornado server for tracking samples at NGI Stockholm

Scripts

Miscellaneous scripts, very much WIP and not intended for anyone else to use.

irma-provision

Ansible playbooks for provisioning NGI pipeline and related sw

maxulysse.github.io

My own jekyll personnal website

MultiQC

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

MultiQC_NGI

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

MultiQC_TestData

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

Nextflow_test

Toy repository to replicate bugs

NF_FineStructure

A nextflow wrapper for running FineStructure

NGI-NextflowDocs

Common documentation for National Genomics Infrastructure pipelines built with Nextflow

NGI-RNAseq

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

ngi_pipeline

Code driving the production pipeline at SciLifeLab

ngi_visualizations

Next-Gen Sequencing Visualisation Scripts.

oneliners_and_scripts

Popolipo

Publications

Simple web-based publications reference database system.

r_stuff

rfmix

RFMIX - Local Ancestry and Admixture Inference Version 2

scilifelab_epps

A collection of Genologics Clarity LIMS EPPs used at Scilifelab.

seek

For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.

standalone_scripts

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

TACA

Tool for the Automation of Cleanup and Analyses

testing

Showing how github works