jharenza
Principal Investigator of the Rokita Lab and Director of the Brain Tumor Institute Bioinformatics Core
Children's National HospitalWashington, D.C.
Pinned Repositories
annoFuse
Filter and prioritize fusion calls
ATAC
atSNP
Large-scale testing for SNP-motif interactions.
bamtools
C++ API & command-line toolkit for working with BAM data
bard1-wgs
Whole genome sequencing (WGS) analysis for neuroblastoma IMR-5 cell lines carrying rare, pathogenic BARD1 variants introduced by CRISPR
Light-Dark-Box-Analysis
R script for analyzing behavioral data from MedAssociates Light-Dark chambers.
NBL-cell-line-RNA-seq
jharenza's Repositories
jharenza/annoFuse
Filter and prioritize fusion calls
jharenza/atSNP
Large-scale testing for SNP-motif interactions.
jharenza/bard1-wgs
Whole genome sequencing (WGS) analysis for neuroblastoma IMR-5 cell lines carrying rare, pathogenic BARD1 variants introduced by CRISPR
jharenza/NBL-cell-line-RNA-seq
jharenza/bioinfo
Various bioinformatics tools
jharenza/ChIP-Seq
jharenza/deep-review
A collaboratively written review paper on deep learning, genomics, and precision medicine
jharenza/disambiguate
Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem
jharenza/drive-template
PI drive cookiecutter template
jharenza/ea-utils
Automatically exported from code.google.com/p/ea-utils
jharenza/handbook
📖 Technical best practices in D3b
jharenza/illumina-utils
A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
jharenza/jharenza.github.io
jharenza/maftools
:cancer: Summarize, Analyze and Visualize MAF files from TCGA or in house studies.
jharenza/mageri-paper
Data and post-analysis for MAGERI project
jharenza/mnp_training
DNA methylation-based classification of central nervous system tumours
jharenza/ngs-filters
Filters for false-positive mutation calls in NGS
jharenza/NucleoATAC
nucleosome calling using ATAC-seq
jharenza/oncokb-annotator
Annotates variants in MAF with OncoKB annotation.
jharenza/OpenPBTA-analysis
The analysis repository for the Open Pediatric Brain Tumor Atlas Project
jharenza/OpenPBTA-manuscript
The manuscript repository for the Open Pediatric Brain Tumor Atlas Project
jharenza/pptc-pdx-ethnicity-inference
Ethnicity inference for Pediatric Preclinical Testing Consortium (PPTC) patient-derived xenograft models
jharenza/project-template
CHOP project template
jharenza/rasqual
Robust Allele Specific Quantification and quality controL
jharenza/reg-gen
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
jharenza/RNAseqDB
jharenza/sunburstR
R htmlwidget for interactive sunburst plots
jharenza/targetfinder
jharenza/toil-rnaseq
UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
jharenza/umi
Preprocessing tools for unique molecular index (UMI) sequencing reads