edawson

Senior Scientist in Genomics, HPC and AI @nvidia

@nvidiaNew York City

Pinned Repositories

check-sex
Determine the biological sex of a human whole-genome BAM file
Language:Dockerfile12 1 49
gfakluge
A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
Language:C++51 3 4220
gram
Parse, manipulate, and emit GRAM (graph read alignment/map format)
Language:C++3 2 00
mkmh
Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
Language:C++24 2 42
rkmh
Classify sequencing reads using MinHash.
Language:C++47 6 124
svaha
Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]
Language:C++11 1 71
svaha2
Linear-time, low-memory construction of variation graphs
Language:C++18 0 50
tidysig
A tidyverse-style package for plotting mutational signatures and context counts.
Language:R3 1 121
vg
tools for working with genome variation graphs
Language:C++1.1k 48 2k191

edawson's Repositories

edawson/gfakluge
A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
Language:C++51 3 4220
edawson/svaha
Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]
Language:C++11 1 71
edawson/pliib
A hacky little C++ library that holds some useful functions.
Language:C++3 1 24
edawson/sv-exercise-1
A short exercise for learning to work with structural variants in VCF format
3 1 0
edawson/bam-matcher
Language:Python2 1 21
edawson/dawdl
WDL library for common bioinformatics tasks
Language:WDL1 2 1
edawson/kseqpp
Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)
Language:C++1 1 0
edawson/sv-tutorial-2
A tutorial on calling structural variants with SVABA
1 1 0
edawson/tinyFA
A header-only C++ FASTA parser and indexer
Language:C++1 1 02
edawson/1brc
1️⃣🐝🏎️ The One Billion Row Challenge -- A fun exploration of how quickly 1B rows from a text file can be aggregated with Java
Language:Java0 0
edawson/compact_vector
Bit packed vector of integral values
Language:C++0 0
edawson/cromrunner
A scheduler / meta-manager for running multiple Cromwell instances on a single WDL workflow in parallel.
Language:Python1 1
edawson/cromwell-accountant
A script to calculate estimated cost of a Cromwell workflow on Google Cloud
edawson/enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
Language:Python0 0
edawson/examples
A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.
edawson/gatk
Official code repository for GATK versions 4 and up
Language:Java0 0
edawson/helpy
A random collection of python scripts which are easier than fighting the equivalent shell commands
Language:Python1 0
edawson/hugo-serif-theme
Serif is a modern business theme for Hugo.
Language:SCSS0 0
edawson/mio
Cross-platform C++11 header-only library for memory mapped file IO
Language:C++0 0
edawson/pip2poetry
Convert a requirements.txt file to a poetry.lock file
Language:Python1 0
edawson/presig
Convert MAF files to formats used as input to mutational signature programs including SigProfiler
Language:Python1 0
edawson/ProteinMPNN
Code for the ProteinMPNN paper
Language:Jupyter Notebook0 0
edawson/puretabix
Language:Python0 0
edawson/r2-public-worker
Cloudflare Worker to make a R2 Bucket public!
edawson/RatesTools
Pipeline to calculate de novo mutation rates from parent-offspring trios
Language:Ruby0 0
edawson/saas
Build your own SaaS business with SaaS boilerplate. Productive stack: React, Material-UI, Next, MobX, WebSockets, Express, Node, Mongoose, MongoDB. Written with TypeScript.
Language:TypeScript0 0
edawson/SigProfilerHelper
Helper scripts for the SigProfiler suite of mutational signature analysis tools
Language:Python1 2
edawson/Spectre
Copy number caller for long read data including SNV utilization
Language:Python
edawson/storage-consumption-calculator
An R shiny app for calculating the energy used when storing a specified amount of data.
Language:R
edawson/svaba
Structural variation and indel detection by local assembly
Language:C++0 0