zongchangli Goto Github PK

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

emagma-tutorial

A step by step guide on how to use eMAGMA, an approach to conducting eQTL informed gene-based tests.

epigenetic_ageing_clock

Biological insights into the epigenetic ageing clock

gat

Genomic Association Tester

gene_lists

List of gene lists for genomic analyses.

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

h-magma

jitterbug

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.

ldsc

LD Score Regression (LDSC)

liu2020proteincell

Pipeline & Reproducible analysis examples for amplicon and metagenome in microbiome

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

mega

methylpy

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

microbiomeprotocol

Microbiome Protocol eBook related documents and scripts.

miqtl_cookbook

mosaicforecast

A mosaicSNV detecting software based on phasing and random forest

mutationalpatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues

my_wgcna

nmagma

Codes and data used in nMAGMA, an approach to intergrate Hi-C, eQTL and gene networks inferred from WGCNA into original MAGMA annotation.

poolr

Package for pooling the results from (dependent) tests