Pinned Repositories
aneufinder
Find CNVs in single cell sequencing data.
awesome-single-cell
List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
bits
BITS: Binary Interval Search
cause
R package for CAUSE
CCGWAS
chip-seq-pipeline
ENCODE Uniform processing pipeline for ChIP-seq
ComprehensiveMultiOmicsAnalysis_MZDSCZ
Integrative analysis of genome (WGS), methylome(WGBS), transcriptome(RNA-seq) and proteome data to investigate the genetic mechanisms to underlying monozygotic twin pairs discordant for schizophrenia
CpG_Me
A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)
cwas
defining_genomic_regions
Define regions in the genome
zongchangli's Repositories
zongchangli/ComprehensiveMultiOmicsAnalysis_MZDSCZ
Integrative analysis of genome (WGS), methylome(WGBS), transcriptome(RNA-seq) and proteome data to investigate the genetic mechanisms to underlying monozygotic twin pairs discordant for schizophrenia
zongchangli/aneufinder
Find CNVs in single cell sequencing data.
zongchangli/awesome-single-cell
List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
zongchangli/cause
R package for CAUSE
zongchangli/CCGWAS
zongchangli/CpG_Me
A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)
zongchangli/eMAGMA-tutorial
A step by step guide on how to use eMAGMA, an approach to conducting eQTL informed gene-based tests.
zongchangli/epigenetic_ageing_clock
Biological insights into the epigenetic ageing clock
zongchangli/gtex-pipeline
GTEx & TOPMed data production and analysis pipelines
zongchangli/H-MAGMA
zongchangli/ldsc
LD Score Regression (LDSC)
zongchangli/Liu2020ProteinCell
Pipeline & Reproducible analysis examples for amplicon and metagenome in microbiome
zongchangli/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in house studies.
zongchangli/methylpy
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
zongchangli/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
zongchangli/MicrobiomeProtocol
Microbiome Protocol eBook related documents and scripts.
zongchangli/miQTL_cookbook
zongchangli/MosaicForecast
A mosaicSNV detecting software based on phasing and random forest
zongchangli/MutationalPatterns
R package for extracting and visualizing mutational patterns in base substitution catalogues
zongchangli/nMAGMA
Codes and data used in nMAGMA, an approach to intergrate Hi-C, eQTL and gene networks inferred from WGCNA into original MAGMA annotation.
zongchangli/poolR
Package for pooling the results from (dependent) tests
zongchangli/RCircos
:exclamation: This is a read-only mirror of the CRAN R package repository. RCircos — Circos 2D Track Plot. Homepage: http://bitbucket.org/henryhzhang/rcircos
zongchangli/RNASeq
RNASeq pipeline
zongchangli/rnaseq-1
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
zongchangli/scan-snv
Single cell somatic genotyper
zongchangli/scGRN
zongchangli/snfpy
Similarity network fusion in Python
zongchangli/SZ_methylation
zongchangli/wg-blimp
wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data
zongchangli/wgbs-pipeline
ENCODE whole-genome bisulfite sequencing (WGBS) pipeline