Liang Ma's repositories
Atac-seq_Quality_Control_pipe
Atac-seq QC matrix
atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
Cas9FateMapping
Collection of code for the GESTALT fate mapping paper using the CRISPR/Cas9 system
chipseq_pipeline
AQUAS TF and histone ChIP-seq pipeline
COS_public_release
Public release of code for analysis of RNA-Seq data from COS cohort
DDDNonCoding2017
Code for paper published in March, 2017 analysing the role of de novo mutations in severe developmental disorders (part of the deciphering developmental disorders project).
Genome-wide-changes-in-lncRNA-alternative-splicing-and-cortical-patterning-in-autism
Human Postmortem ASD RNA-seq Analysis Parikshak et al 2016
getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
gtex-pipeline
GTEx Consortium data production and analysis pipelines
pipelines_for_ChIP-seq_analysis
Pipelines for ChIP-seq analysis, such as peak calling, differential enrichment detection, and pausing index calculation for PolII.
Python_for_Data_Science
A rapid on-ramp primer for programmers who want to learn Python for doing data science research and development.
SPEAQeasy
SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.
styles
Official repository for Citation Style Language (CSL) citation styles.
tabula-muris
Code and annotations for the Tabula Muris single-cell transcriptomic dataset.