The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. The links listed in this directory are selected on the basis of recommendations from bioinformatics experts in the field. We also rely on input from our community of bioinformatics users for suggestions. Starting in 2003, we have also started listing all links contained in the NAR Webserver issue.……【阅读全文】

The LONI Pipeline is a free workflow application primarily aimed at neuroimaging researchers. With the LONI Pipeline users can quickly create workflows that take advantage of all the greatest neuroimaging tools available.……【阅读全文】

注：说是“生物信息学培训”，其实就是我在实验室内部的Journal Club上做的入门级别的生物信息学介绍。……【阅读全文】

• 简介（摘自官网）

The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis.……【阅读全文】

• 简介

bedtools总共有二三十个工具/命令来处理基因组数据。比较典型而且常用的功能举例如下：
格式转换，bam转bed（bamToBed），bed转其他格式（bedToBam，bedToIgv）；
对基因组坐标的逻辑运算，包括：交集（intersectBed，windowBed），”邻集“（closestBed），补集（complementBed），并集（mergeBed），差集（subtractBed）;
计算覆盖度（coverage）（coverageBed，genomeCoverageBed）；
此外，还有一些强大而实用的工具（shuffleBed，groupBy，annotateBed，……）。……【阅读全文】