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Liang Ma's starred repositories

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

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circlize

Circular visualization in R

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ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

Language:PythonMIT727 65 12

MACS

MACS -- Model-based Analysis of ChIP-Seq

Language:CythonBSD-3-Clause697 50 522

SpliceAI

A deep learning-based tool to identify splice variants

Language:PythonNOASSERTION395 21 136

Intro-to-ChIPseq

Intro to ChIPseq using HPC

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annotables

R data package for annotating/converting Gene IDs

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chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline

Language:JavaBSD-3-Clause105 40 43

WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery

Language:PythonApache-2.0102 11 99

GeneticsMakie.jl

🧬High-performance genetics- and genomics-related data visualization using Makie.jl

Language:JuliaMIT77 4 5

xqtl-protocol

Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium

Language:Jupyter NotebookMIT38 5 263

singlecell_neuroseq_paper

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

Language:Jupyter NotebookApache-2.021 6 1

MoSEA

Motif Scan and Enrichment Analysis (MoSEA)

Language:PythonISC16 4 6

mrlocus

Older repo for MRLocus. See new website for software usage guide:

Language:R15 2 7

MMQTL

MMQTL is a statistical package applying meta-analysis to detect multiple QTL signals integrating signals among conditions, with control for population structure and relatedness

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cnvkit_pipeline

call copy number from WES(WXS)

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Alzheimers_DNAm

Epigenome-wide analysis of DNA methylation from Alzheimer's patients and unaffected controls

Language:RMIT9 5 2

GWAS-QC

Quality control steps for GWAS

Language:Shell9 4 1

SuRE-SNV-code

collection of repos' holding code associated with manuscript J. van Arensbergen et al: Systematic identification of human SNPs affecting regulatory element activity.

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