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Chengran Yang (cyang-2014)

cyang-2014

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Company:Washington University in St. Louis

Location:St. Louis, MO

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Chengran Yang's repositories

cutadapt

cutadapt removes adapter sequences from sequencing reads

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activityinequality

Data release for Activity Inequality paper

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chromVAR

chromatin Variability Across Regions (of the genome!)

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chromVARmotifs

R package with motifs for use with chromVAR

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cooler

A cool place to store your Hi-C

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cshl-singlecell-2017

Single Cell Analysis course at Cold Spring Harbor Laboratory 2017

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distmap

DistMap

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dropbead

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fiveMinuteStats

A repo of short "vignettes" illustrating statistical concepts

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ggjoy

Geoms to make joy plots using ggplot2

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Giotto

Single-cell spatial analysis pipeline

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GTExV6PRareVariation

Repository to reproduce analyses from the GTEx V6P Rare Variation Manuscript

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HiC_AB_Compartments_Mouse

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keras

Deep Learning library for Python. Runs on TensorFlow, Theano, or CNTK.

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Mandalorion

Analysis Pipeline to analyze Nanopore RNAseq data

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MAST

Tools and methods for analysis of single cell assay data in R

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MetaNeighbor

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motifmatchr

Fast motif matching in R

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Plasma2omic2pops

Scripts for the manuscript "European and African stratified plasma protein-QTL and metabolite-QTL analyses identify ancestry-specific T2D effector proteins and metabolites"

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Publications

Scripts used in published papers

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sambamba

Tools for working with SAM/BAM data

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scanpy

Single-Cell Analysis in Python. Scales to very high cell numbers.

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SCENIC

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scRNAseq-Malaria

Codes associated with the Poran et al. paper titled "Single-cell RNA-seq reveals a signature of sexual commitment in malaria parasites".

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slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell sequencing data.

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systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool

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t81_558_deep_learning

Washington University (in St. Louis) Course T81-558: Applications of Deep Neural Networks

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TENxGenomics

Interface to 10x Genomics' 1.3 m single cell data set

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velocyto.R

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wordcloud2

R interface to wordcloud for data visualization.

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