Pinned Repositories
cscripts
Miscalanious C and C++ scripts.
GrNMF
An R/Rcpp/RcppArmadillo implementation of Deng Cai's Non-negative Matrix Factorization on Manifold, sometimes called GNMF or GrNMF.
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Subset of the kent source libraries (perhaps out of date) that are easily built and installed on OSX and Linux.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.
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.
re-pair
Program to re-do the pairing of fastq reads. This program is modified from http://code.google.com/p/ngopt/source/browse/trunk/tools/pair_reads/repair.cpp?r=85
SeqPrep
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
SimSeq
An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.
swift-c-htslib
Ultra-light HTSLIB wrapper for swift, currently just a modulemap giving you access to the C functions.
jstjohn's Repositories
jstjohn/SeqPrep
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
jstjohn/IntroToStatisticalLearningR-
Work on Introduction to Statistical Learning
jstjohn/swift-c-htslib
Ultra-light HTSLIB wrapper for swift, currently just a modulemap giving you access to the C functions.
jstjohn/swift-c-htslib-example
Example swift package built against CHTSLib
jstjohn/cutadapt
cutadapt removes adapter sequences from sequencing reads
jstjohn/quora_querstion_pairs_kaggle
jstjohn/signalstepdetector
Automatically exported from code.google.com/p/signalstepdetector
jstjohn/avocado
A Variant Caller, Distributed. Apache 2 licensed.
jstjohn/bayesian-machine-learning
Notebooks related to Bayesian methods for machine learning
jstjohn/cyber-dojo
Free in-browser coding-dojo, running live at
jstjohn/deepomics
deep learning toolkit (written on top of tensorflow) to streamline computational biology analysis
jstjohn/dnc
A TensorFlow implementation of the Differentiable Neural Computer.
jstjohn/DNC-tensorflow
A TensorFlow implementation of DeepMind's Differential Neural Computers (DNC)
jstjohn/docker-formula
Install and set up Docker
jstjohn/enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
jstjohn/fonolo4android-lite
Automatically exported from code.google.com/p/fonolo4android-lite
jstjohn/fpinscala
Code, exercises, answers, and hints to go along with the book "Functional Programming in Scala"
jstjohn/latent-diffusion
High-Resolution Image Synthesis with Latent Diffusion Models
jstjohn/Megatron-LM
Ongoing research training transformer models at scale
jstjohn/NeMo
NeMo: a framework for generative AI
jstjohn/playground
Play with neural networks!
jstjohn/pybedtools
Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
jstjohn/pyston
An open-source Python implementation using JIT techniques.
jstjohn/pytorch
Tensors and Dynamic neural networks in Python with strong GPU acceleration
jstjohn/pytorch-lightning
The lightweight PyTorch wrapper for high-performance AI research. Scale your models, not the boilerplate.
jstjohn/pytorch-optimizer
torch-optimizer -- collection of optimizers for Pytorch
jstjohn/quotebookr
Automatically exported from code.google.com/p/quotebookr
jstjohn/rust-seqprep
jstjohn/scVI-dev
Development branch of the scVI project in PyTorch
jstjohn/x-transformers
A simple but complete full-attention transformer with a set of promising experimental features from various papers