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Javier Díez Pérez's Projects

bcbb icon bcbb

Useful bioinformatics code, primarily in Python and R

biopython icon biopython

Official git repository for Biopython (converted from CVS)

dgi-db icon dgi-db

Rails frontend to The Genome Institute's drug gene interaction database.

favr icon favr

Filtering and Annotation of Variants that are Rare

gatk-protected icon gatk-protected

GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only

gemini icon gemini

a lightweight db framework for disease and population genetics.

geocompr icon geocompr

Forthcoming book on geographic data with R

hts-specs icon hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

illumina-utils icon illumina-utils

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).

ngsutils icon ngsutils

Tools for next-generation sequencing analysis

oncotator icon oncotator

Large-file conversion with http://www.broadinstitute.org/oncotator

pybedtools icon pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

pyvcf icon pyvcf

A Variant Call Format reader for Python.

qiime icon qiime

Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests

rq icon rq

Simple job queues for Python

rubra icon rubra

Infrastructure code to support DNA pipeline

seqtk icon seqtk

Toolkit for processing sequences in FASTA/Q formats

shiny icon shiny

Easy interactive web applications with R

tablefactory icon tablefactory

Easily create HTML, spreadsheet, or PDF tables from common Python data sources

vcflib icon vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

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