生信行业有很多大牛，他们把某个方向分析整理成了一个个workflow（流程），有了流程，我们学习生信就更加有整体性。
生信初学者常常犯的一个毛病，就是很多概念和方法，拆开知道怎么回事，但是缺乏把这些概念和方法串联成一个流程的能力。所以本文将整理一些网络上的优质workflow来方便大家的学习。
如果你遇到不错的流程，欢迎在留言区留言，或者邮件我：
郑宝童
btzheng11165@163.com

一、Bioconductor系列workflow（x22）

• AnnotationWorkflow (2)

Package	Maintainer	Title	Rank
annotation	Bioconductor Package Maintainer	Genomic Annotation Resources	5
variants	Bioconductor Package Maintainer	Annotating Genomic Variants	11

• BasicWorkflow (4)

Package	Maintainer	Title	Rank
arrays	Bioconductor Package Maintainer	Using Bioconductor for Microarray Analysis	10
BiocMetaWorkflow	Mike Smith	BioC Workflow about publishing a Bioc Workflow	22
liftOver	Bioconductor Package Maintainer	Changing genomic coordinate systems with rtracklayer::liftOver	7
sequencing	Martin Morgan	Introduction to Bioconductor for Sequence Data	8

• EpigeneticsWorkflow (3)

Package	Maintainer	Title	Rank
chipseqDB	Aaron Lun	From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data	16
generegulation	Bioconductor Package Maintainer	Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching	15
methylationArrayAnalysis	Jovana Maksimovic	A cross-package Bioconductor workflow for analysing methylation array data.	6

• GeneExpressionWorkflow (7)

Package	Maintainer	Title	Rank
EGSEA123	Matthew Ritchie	Easy and efficient ensemble gene set testing with EGSEA	16
ExpressionNormalizationWorkflow	Karthikeyan Murugesan	Gene Expression Normalization Workflow	14
maEndToEnd	Bernd Klaus	An end to end workflow for differential gene expression using Affymetrix microarrays	21
RNAseq123	Matthew Ritchie	RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR	2
rnaseqDTU	Michael Love	RNA-seq workflow for differential transcript usage following Salmon quantification	22
rnaseqGene	Michael Love	RNA-seq workflow: gene-level exploratory analysis and differential expression	1
RnaSeqGeneEdgeRQL	Yunshun Chen	Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipeline	12

• GenomicVariantsWorkflow (1)

Package	Maintainer	Title	Rank
eQTL	Vincent Carey	Cloud-enabled cis-eQTL searches with Bioconductor GGtools 5.x	19

• ProteomicsWorkflow (2)

Package	Maintainer	Title	Rank
highthroughputassays	Bioconductor Package Maintainer	Using Bioconductor with High Throughput Assays	18
proteomics	Laurent Gatto	Mass spectrometry and proteomics data analysis	9

• ResourceQueryingWorkflow (1)

Package	Maintainer	Title	Rank
TCGAWorkflow	Tiago Chedraoui Silva	TCGA Workflow Analyze cancer genomics and epigenomics data using Bioconductor packages	4

• SingleCellWorkflow (2)

Package	Maintainer	Title	Rank
cytofWorkflow	Malgorzata Nowicka	CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets	13
simpleSingleCell	Aaron Lun	A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor	3

二、待输入

1.NGS data analysis with R / Bioconductor: ChIP-Seq workflow
2.NGS sequence analysis with R / Bioconductor: RNA-Seq workflow