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Javier Quilez Oliete's Projects

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A place to share how I solved questions that I could not quickly find in Google and/or took me some time to figure out.

cgat icon cgat

CGAT - Computational Genomics Analysis Tools

fastqc icon fastqc

Bash scripts and Ipython notebook for running the FASTQC program over multiple samples and analyze its quality control reports

plotting icon plotting

Python scripts (mostly) to generate plots using genomic data

svtyper icon svtyper

Bayesian genotyper for structural variants

tadbit icon tadbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

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