Pinned Repositories
atlas-snp_old
SNP detection for NGS
bamtools
API and toolkit for reading, writing, and manipulating BAM (genome alignment) files
bcbb
Useful bioinformatics code, primarily in Python and R
dotfiles
.files
ExomePipe
WGS and Exome analysis pipeline
fermi
Yet another de novo assembler based on the FM-index
khmer
in-memory k-mer counting
PARABL
Parametric Bayesian Likelihood
public_html
scripts
Zinfandel
CNV genotyping from resequencing data
joshuashen's Repositories
joshuashen/public_html
scripts
joshuashen/dotfiles
.files
joshuashen/fermi
Yet another de novo assembler based on the FM-index
joshuashen/aloft
ALOFT, the Annotation Of Loss-of-Function Transcripts, provides extensive functional annotations to loss-of-function variants in the human genome.
joshuashen/atlas-snp
Automatically exported from code.google.com/p/atlas-snp
joshuashen/BayesDB
A Bayesian database for querying the probable implications of data as easily as SQL databases query the data itself
joshuashen/bgt
Flexible genotype query among 30,000+ samples whole-genome
joshuashen/bioawk
BWK awk modified for biological data
joshuashen/breast_cancer_panel
Breast Cancer Study
joshuashen/BSMS205_2019Spring
BSMS205 Genetics - 2019 Spring
joshuashen/CANOES
fork this to get a repo with only a gh-pages branch that is easy to edit
joshuashen/cbioportal
joshuashen/d3
A JavaScript visualization library for HTML and SVG.
joshuashen/exac_browser
Browser for ExAC consortium data
joshuashen/gcn
Implementation of Graph Convolutional Networks in TensorFlow
joshuashen/gqt
A genotype query interface.
joshuashen/gxbrowser
BRI Gene Browser for integrating Microarray, RNA-seq data, expression data with demographic and clinical information
joshuashen/lof
LoF
joshuashen/lumpy-sv
lumpy: a general probabilistic framework for structural variant discovery
joshuashen/manta
Structural variant and indel caller for mapped sequencing data
joshuashen/Missense-DNN
DNN for classifying functional consequence of missense genetic mutations using an ensemble of other scoring methods
joshuashen/MutationClusterVisualization
joshuashen/PSAP-pipeline
joshuashen/rafalib
joshuashen/ResearchKit
ResearchKit is an open source software framework that makes it easy to create apps for medical research or for other research projects.
joshuashen/rHealthDataGov
This package provides an R interface to the HealthData.gov data API.
joshuashen/steady
Best-practice pipelines for fully automated high throughput sequencing analysis
joshuashen/VariantFilterScripts
joshuashen/whisper
Robust Speech Recognition via Large-Scale Weak Supervision
joshuashen/xlsx2csv
Convert xslx to csv, it is fast, and works for huge xlsx files