Pinned Repositories
activityinequality
Data release for Activity Inequality paper
AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
allelecounter
Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP.
AlleleSpecificATACseq
atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
BackSPIN
Biclustering algorithm
bedtools-python
A Python interface to the BEDTools API using Cython
bfc
High-performance error correction for Illumina resequencing data
cutadapt
cutadapt removes adapter sequences from sequencing reads
cyang-2014's Repositories
cyang-2014/cutadapt
cutadapt removes adapter sequences from sequencing reads
cyang-2014/activityinequality
Data release for Activity Inequality paper
cyang-2014/chromVAR
chromatin Variability Across Regions (of the genome!)
cyang-2014/chromVARmotifs
R package with motifs for use with chromVAR
cyang-2014/cooler
A cool place to store your Hi-C
cyang-2014/CSFprotQTLbenchmark
Benchmarking the eight models for mapping a large-scale EUR CSF pQTL dataset varying tools, covariates, and protein-normalization strategies
cyang-2014/cshl-singlecell-2017
Single Cell Analysis course at Cold Spring Harbor Laboratory 2017
cyang-2014/distmap
DistMap
cyang-2014/dropbead
cyang-2014/fiveMinuteStats
A repo of short "vignettes" illustrating statistical concepts
cyang-2014/ggjoy
Geoms to make joy plots using ggplot2
cyang-2014/Giotto
Single-cell spatial analysis pipeline
cyang-2014/GTExV6PRareVariation
Repository to reproduce analyses from the GTEx V6P Rare Variation Manuscript
cyang-2014/HiC_AB_Compartments_Mouse
cyang-2014/keras
Deep Learning library for Python. Runs on TensorFlow, Theano, or CNTK.
cyang-2014/Mandalorion
Analysis Pipeline to analyze Nanopore RNAseq data
cyang-2014/MetaNeighbor
cyang-2014/motifmatchr
Fast motif matching in R
cyang-2014/Plasma2omic2pops
Scripts for the manuscript "European and African stratified plasma protein-QTL and metabolite-QTL analyses identify ancestry-specific T2D effector proteins and metabolites"
cyang-2014/Publications
Scripts used in published papers
cyang-2014/sambamba
Tools for working with SAM/BAM data
cyang-2014/scanpy
Single-Cell Analysis in Python. Scales to very high cell numbers.
cyang-2014/SCENIC
cyang-2014/scRNAseq-Malaria
Codes associated with the Poran et al. paper titled "Single-cell RNA-seq reveals a signature of sexual commitment in malaria parasites".
cyang-2014/slingshot
Functions for identifying and characterizing continuous developmental trajectories in single-cell sequencing data.
cyang-2014/systemsgenetics
Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
cyang-2014/t81_558_deep_learning
Washington University (in St. Louis) Course T81-558: Applications of Deep Neural Networks
cyang-2014/TENxGenomics
Interface to 10x Genomics' 1.3 m single cell data set
cyang-2014/velocyto.R
cyang-2014/wordcloud2
R interface to wordcloud for data visualization.