jstjohn Goto Github PK
Name: John St. John
Type: User
Company: Nvidia
Location: Santa Clara, CA
John St. John's Projects
adam
A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
amazonaccess
Amazon Employee Access Challenge
avocado
A Variant Caller, Distributed. Apache 2 licensed.
bayesian-machine-learning
Notebooks related to Bayesian methods for machine learning
clonehd
High-definition reconstruction of clonal composition from next-generation sequencing data
cscripts
Miscalanious C and C++ scripts.
cutadapt
cutadapt removes adapter sequences from sequencing reads
cyber-dojo
Free in-browser coding-dojo, running live at
deepomics
deep learning toolkit (written on top of tensorflow) to streamline computational biology analysis
dnc
A TensorFlow implementation of the Differentiable Neural Computer.
dnc-tensorflow
A TensorFlow implementation of DeepMind's Differential Neural Computers (DNC)
docker-formula
Install and set up Docker
enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
flickribbon
Automatically exported from code.google.com/p/flickribbon
fonolo4android
Automatically exported from code.google.com/p/fonolo4android
fonolo4android-lite
Automatically exported from code.google.com/p/fonolo4android-lite
fpinscala
Code, exercises, answers, and hints to go along with the book "Functional Programming in Scala"
gatk
GATK Official Release Repository
genefamilyfinder
Automatically exported from code.google.com/p/genefamilyfinder
ggplot
ggplot for python
grnmf
An R/Rcpp/RcppArmadillo implementation of Deng Cai's Non-negative Matrix Factorization on Manifold, sometimes called GNMF or GrNMF.
homebrew
The missing package manager for OS X.
introtostatisticallearningr-
Work on Introduction to Statistical Learning
jellyfish
Fork of the jellyfish kmer counter. Here is the description copied from their site: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish stats" command. See the documentation below for more details.
kentlib
Subset of the kent source libraries (perhaps out of date) that are easily built and installed on OSX and Linux. These libraries provide usefull utilities for bioinformatics programming in C. This may contain some of my own libraries for bioinformatics utilities as well as long as they install easily on both my mac and linux box.
kinectorbit
A fork of http://www.arduinoandkinectprojects.com/kinectorbit with an attempt at upgrading to Processing v2.
latent-diffusion
High-Resolution Image Synthesis with Latent Diffusion Models
mia
MIA is an reference guided assembler for DNA reads as generated by recent sequencing technologies. It is designed to support unusual short reads like they come from ancient, fragmented DNA.
nemo
NeMo: a framework for generative AI
playground
Play with neural networks!
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