uio-bmi/bmi_python_sample_project

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uio-bmi/bmi_python_sample_project

uio-bmi

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

immuneML

immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.

compairr

Comparison of Adaptive Immune Receptor Repertoires

two_step_graph_mapper

graph_peak_caller

ChIP-seq peak caller for reads mapped to a graph-based reference genome

dagsim

A framework and specification language for simulating data based on graphical models

pyvg

Importing vg json graphs to Python data structures.

NucBreak

Location of structural errors in a genome assembly and structural variations between a pair of genomes

CausalAIRR

NucMerge

Genome assembly quality improvement assisted by alternative assemblies and paired-end Illumina reads

numpy_alignments

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

variant_calling_benchmarks_two_step_mapper

Scripts for reproducing the variant calling benchmarks presented in the two step mapper paper.

kmercount

Simple kmer counter using Bloom filter and efficient hash function

fdr_under_dependencies

Jupyter Notebook

StarSignDNA

crypt4gh

Crypt4GH standard implementation

in1000-referanseoppgaver

Oppgaver til referanser i in1000

localega-broker

SynthPwr

Synthetic framework for stress testing the parameters and statistical power of epigenetic power calculators

similarity-measures

Code for the similarity measures article

immuneml_tools

Galaxy tools using the immuneML conda package.

track_rand

Track randomization code

compairr-benchmarking

sfb_knowledgebase

Knowledge base with links to relevant resources by the Centre for Bioinformatics, UiO.

statistical_genomics_exercises

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.

cookiecutter-python-research-project

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

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

pharmacoepi_simulation_workshop

The material for the simulation session at the (Epi)genetics in Pharmacoepidemiology workshop

Jupyter Notebook