Pinned Repositories
bionumpy
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
npstructures
genotyping-benchmarking
Snakemake-pipeline for benchmarking genotypers
graph_kmer_index
Simple python kmer index for graphs
graph_read_simulator
Simple diploid read simulator using genome graphs
kmer_mapper
Simple numpy/cython based kmer mapper for mapping kmers from a fasta file to an index
privvg-challenge
shared_memory_wrapper
Simple wrapper around the Shared Array library
vcfmap
kage
Alignment-free genotyper for SNPs and short indels, implemented in Python.
ivargr's Repositories
ivargr/genotyping-benchmarking
Snakemake-pipeline for benchmarking genotypers
ivargr/graph_read_simulator
Simple diploid read simulator using genome graphs
ivargr/kmer_mapper
Simple numpy/cython based kmer mapper for mapping kmers from a fasta file to an index
ivargr/privvg-challenge
ivargr/graph_kmer_index
Simple python kmer index for graphs
ivargr/shared_memory_wrapper
Simple wrapper around the Shared Array library
ivargr/vcfmap
ivargr/kage-indexing
Snakemake pipeline for creating indexes for the KAGE genotyper
ivargr/bionumpy-example-data
Example data for BioNumPy
ivargr/bionumpy_snp_kmer_filtering_example
ivargr/bios3010-python
Exercises and teaching material for the Python part of bios3010
ivargr/copilot_testproject
ivargr/CoV_Sequences
SARS-CoV-2 genome from Nigeria
ivargr/FastQC
A quality control analysis tool for high throughput sequencing data
ivargr/hic-assembly-benchmarking
ivargr/hierarchical_results
Simple test of a hierarchical disk-backed logger
ivargr/in1000-crafts-public
ivargr/javascript-winwheel
Create spinning prize wheels on HTML canvas with Winwheel.js
ivargr/kage2-manuscript
ivargr/obgraph
Simple offsetbased graph implementation using Numpy
ivargr/open-the-lid-chip-seq-analysis
Scripts and guide for reproducing the ChIP-seq analysis in Open the LID: LXRα regulates ChREBPα transactivity in a target gene-specific manner through an agonist-modulated LBD-LID interaction
ivargr/paragraph
Graph realignment tools for structural variants
ivargr/python-bioinformatics
Modules for Python in bioinformatics
ivargr/rootstock
Clone me to create your Manubot manuscript
ivargr/sim3C
Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
ivargr/simple_read_mutator
Fast and simple python module for adding SNVs and Indels to a sequence
ivargr/snakehelp
ivargr/snakemake-debugging
ivargr/sv_accuracy
ivargr/test-ci