Pinned Repositories
2015-04-BARM-Concoct
Running concoct for BARM using snakemake
alneberg
pythonkurs
alneberg.com
Personal (family) web page source code
alneberg.github.io
Personal Blog
anglerfish
Codename: Anglerfish
bu
Bioinformatic Utilities
DWUIR
Demultiplexing With UMIs in the Index Read
CONCOCT
Clustering cONtigs with COverage and ComposiTion
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
genomics-status
Tornado server for tracking samples at NGI Stockholm
alneberg's Repositories
alneberg/public_notebooks
Ipython notebooks shared with the public
alneberg/dotfiles
All my configuration files
alneberg/PolarToFunbeat
Translation of Polar Personal Trainer xml files to csv files that funbeat can consume.
alneberg/charon
Database for IGN projects and samples, with RESTful interface. Built on top of Tornado and CouchDB.
alneberg/uppmax_stats_flask
Toy flask app to investigate some specific uppmax usage stats
alneberg/apeltzer.github.io
My personal homepage running with hugo and academic template.
alneberg/tools
Python package with helper tools for the nf-core community.
alneberg/rnaseq
RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control
alneberg/exoseq
Exome Sequencing analysis pipeline (Work in progress)
alneberg/cookiecutter
Template for your own top-end Nextflow pipeline, customised using Cookiecutter
alneberg/vipr
Assembly and intrahost / low-frequency variant calling for viral samples
alneberg/logos
contains logos for nf-core
alneberg/msc_thesis
alneberg/gattaca-public
Lightweight metagenomic binning
alneberg/scikit-learn
scikit-learn: machine learning in Python
alneberg/subsample_fastq_challenge
alneberg/sillymap
A silly implementation of a short read mapper for course DD3436
alneberg/august19
Homepage
alneberg/eggnog_to
Scripts to transfer your eggnog annotations to ec-numbers via uniprot
alneberg/DESMAN
De novo Extraction of Strains from MetAgeNomes
alneberg/bb2490
Course material for BB2490
alneberg/metagenomics-workshop
Metagenomics Workshop 2014-5-21 to 2014-5-23 at SciLifeLab, Stockholm
alneberg/courses
Course homepages for some of the courses given at SciLifeLab
alneberg/cami_15_03
Cami Challenge
alneberg/msc_thesis.scripts
The scripts used in msc_thesis project.
alneberg/flask-by-example
alneberg/sbw2015
Swedish Bioinformatic Workshop 2015 in Stockholm
alneberg/snakemake-workflows
An experimental repo for common snakemake rules and workflows
alneberg/cogler
Summarise and visualise COG annotations for metagenomic contigs
alneberg/OTU_connecting