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.vimrc

cdlmotif.jl-1

Discover DNA sequence motifs using convolutional dictionary learning

code2motifs.jl

convolutionf16.jl

deepunfoldedcdlmotif.jl

Unfolded convolutional learning for motif discovery

em-toy-examples

A toy example to visualize expectation maximization on a mixture of Gaussian

fasta2onehot.jl

fastaloader.jl

Load fasta files that contain DNA strings and process it for other downstream tasks

fastaprocessing.jl

Fasta file processing for Chip/Clip/MPRA datasets

gaussianprocesses.jl

A Julia package for Gaussian Processes

genomic_benchmark_datasets

quick and dirty script to download the DNA classification dataset and make them to fasta files

greedyalign.jl

kchu25.github.io

research

matrixmerge.jl

Using a population of profiles to approximate the real motifs

moods

MOODS: Motif Occurrence Detection Suite

motifpvalue.jl

Threshold and p-value computations for Position Weight Matrices

motifs.jl

DNA Motif discovery that includes the discovery of flexible (long or gapped) motifs.

rbpmotifscore.jl

seqlogo.jl

Plot position weight matrices (PWM)

seqshuffle.jl

Shuffle the string sequences such that the k-mer frequency is preserved in each string

shanedbscan.jl

non-parametric clustering the quick way

shanegpucountminsketch.jl

A much faster way to enumerate stuff

simdna.jl

Generate simulated DNA sequences for regulatory genomics problems

simulatemotif.jl

sparse-index-tracking

Simple implementation to solve the sparse financial index tracking problem with ADMM

tensor-methods

Tensor decomposition for (symmetric/asymmetric tensor power iterations) for some latent variable models

unfoldcdl.jl

Deep Unfolded Convolutional Dictionary Learning for motif discovery.

useful_stuff

useful scripts for research

visualizemotifs.jl

wustl-latex-dissertation-template

LaTeX disseration and thesis template for The Graduate School at Washington University in St. Louis.