zongchangli

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.

cause

R package for CAUSE

CCGWAS

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)

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

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

H-MAGMA

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.

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

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

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

RNASeq

RNASeq pipeline

rnaseq-1

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

scan-snv

Single cell somatic genotyper

scGRN

snfpy

Similarity network fusion in Python

SZ_methylation

wg-blimp

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data

wgbs-pipeline

ENCODE whole-genome bisulfite sequencing (WGBS) pipeline