Pinned Repositories
gatk
GATK Official Release Repository
iPython_Notebook
gpratt's Repositories
gpratt/gatk
GATK Official Release Repository
gpratt/iPython_Notebook
gpratt/adaptivebiotech_exercise
Programming Exercise for Adaptive Biotech
gpratt/aizawa
Analysis Scripts For Aizawa Lab
gpratt/clipper
A tool to identify CLIP-seq peaks
gpratt/dagr
A scala based DSL and framework for writing and executing bioinformatics pipelines as Directed Acyclic GRaphs
gpratt/fgbio
Tools for working with genomic and high throughput sequencing data.
gpratt/gatk_queue_tutorial
gpratt/gffutils
GFF and GTF file manipulation and interconversion
gpratt/gpratt.github.io
Personal Blog
gpratt/gscripts
General Use Scripts and Helper functions
gpratt/htseq
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
gpratt/khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
gpratt/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
gpratt/nbviewer
Nbconvert as a webservice (rendering ipynb to static HTML)
gpratt/PIPE-CLIP
gpratt/processing_scripts
scripts for processing data
gpratt/pybedtools
Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
gpratt/Ren_Rotation
Code for Ren Lab Rotation
gpratt/sampleproject
A sample project that exists for PyPUG's "Tutorial on Packaging and Distributing Projects"
gpratt/screed
a simple read-only sequence database, designed for short reads
gpratt/shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
gpratt/trackhub
create, manage, and upload track hubs for use in the UCSC genome browser
gpratt/tscc_ipython
gpratt/ucsd-thesis
gpratt/UMI-tools
Tools for handling Unique Molecular Identifiers in NGS data sets