Centre for Bioinformatics, University of Oslo (@uio-bmi)
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Top repositories

1

immuneML

immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
Python
60
star
2

compairr

Comparison of Adaptive Immune Receptor Repertoires
C++
25
star
3

two_step_graph_mapper

Python
21
star
4

graph_peak_caller

ChIP-seq peak caller for reads mapped to a graph-based reference genome
Python
19
star
5

dagsim

A framework and specification language for simulating data based on graphical models
Python
18
star
6

pyvg

Importing vg json graphs to Python data structures.
Python
10
star
7

NucBreak

Location of structural errors in a genome assembly and structural variations between a pair of genomes
Python
9
star
8

CausalAIRR

Python
9
star
9

NucMerge

Genome assembly quality improvement assisted by alternative assemblies and paired-end Illumina reads
Python
7
star
10

numpy_alignments

Simple Python module for efficient storing and comparison of mapped reads using numpy
Python
2
star
11

variant_calling_benchmarks_two_step_mapper

Scripts for reproducing the variant calling benchmarks presented in the two step mapper paper.
Shell
2
star
12

kmercount

Simple kmer counter using Bloom filter and efficient hash function
C++
2
star
13

fdr_under_dependencies

Jupyter Notebook
2
star
14

StarSignDNA

Python
2
star
15

crypt4gh

Crypt4GH standard implementation
Java
2
star
16

in1000-referanseoppgaver

Oppgaver til referanser i in1000
Python
1
star
17

localega-broker

Shell
1
star
18

bmi_python_sample_project

A baseic Python sample project, that can be used to initialize new Python projects
Python
1
star
19

SynthPwr

Synthetic framework for stress testing the parameters and statistical power of epigenetic power calculators
Python
1
star
20

similarity-measures

Code for the similarity measures article
R
1
star
21

immuneml_tools

Galaxy tools using the immuneML conda package.
Python
1
star
22

track_rand

Track randomization code
Python
1
star
23

compairr-benchmarking

Python
1
star
24

sfb_knowledgebase

Knowledge base with links to relevant resources by the Centre for Bioinformatics, UiO.
Python
1
star
25

statistical_genomics_exercises

HTML
1
star
26

VirMake

VirMake is a Snakemake based pipeline that offers viral metagenic data analysis on paired-end data. It offers taxonomic and functional annotation, supports offline running and support for HPC cluster execution. It is made for Linux based systems and has been tested on SLURM cluster execution.
Python
1
star
27

cookiecutter-python-research-project

A cookiecutter for easier continous integration in a research project based on Python code
Python
1
star
28

machine_learning_in_comp_bio_exercises

These exercises are a part of the IN-BIOS5000 course at UiO, for the intro lectures on machine learning in computational biology.
Jupyter Notebook
1
star
29

pharmacoepi_simulation_workshop

The material for the simulation session at the (Epi)genetics in Pharmacoepidemiology workshop
Jupyter Notebook
1
star