yal054
Assistant Professor Washington University School of Medicine
Washington University School of Medicine
yal054's Stars
calico/basenji
Sequential regulatory activity predictions with deep convolutional neural networks.
DataSlingers/iPCA
Integrated Principal Components Analysis
datalad/datalad
Keep code, data, containers under control with git and git-annex
google/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
kundajelab/tfmodisco
TF MOtif Discovery from Importance SCOres
ernstlab/ChromTime
Modeling Spatio-temporal Dynamics of Chromatin Marks
welch-lab/liger
R package for integrating and analyzing multiple single-cell datasets
dixonlab/Taurus-MH
ma-compbio/PEP
ncbi/TPMCalculator
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
kundajelab/bpnet
Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
immunogenomics/LISI
Methods to compute Local Inverse Simpson's Index (LISI)
theislab/kBET
An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
gersteinlab/MatchedFilter
Prediction of Active Enhancers and Promoters in a Cell type specific manner using shape matching of histone and/or DNase-I hypersensitivity profiles
liulab-dfci/MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
dbrg77/scATAC_snakemake
Snakemake pipeline for plate scATAC-seq processing
maximilianh/cellBrowser
main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
igvteam/igv.js
Embeddable genomic visualization component based on the Integrative Genomics Viewer
mukamel-lab/SingleCellFusion
SingleCellFusion--a tool to integrate single-cell transcriptome and epigenome data
FangmingXie/mctseq_over_under_splitting
Analysis of over- and under-splitting of clustering for snmC2T-seq datasets
poloclub/cnn-explainer
Learning Convolutional Neural Networks with Interactive Visualization.
aidenlab/juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
gkichaev/PAINTOR_V3.0
Fast, integrative fine mapping with functional data
YeoLab/gscripts
General Use Scripts and Helper functions
GreenleafLab/chromVARmotifs
R package with motifs for use with chromVAR
da-bar/JASPAR2020
JASPAR2020 data package
khodosevichlab/CellAnnotatoR
Automated marker-based annotation of cell types
cosmoharrigan/matrix-entropy
Python implementation of "Measuring entropy/ information/ patterns of a 2d binary matrix" based on the corresponding StackOverflow answer
broadinstitute/ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
hr1912/TreeExp
TreeExp 2.0: Toolbox for analyzing expression evolution based on RNA-seq count data