Preface

Just some basic install commands and settings to setup my jupyter lab.

Preface

Actually this post works as a link to one of crazyhottommy‘s posts which answered a lot of questions of transcripts quantificaiton that have haunted me for a long time.

前言/Abstract

RNA velocity in single cells

作者是瑞典医学院的 Sten Linnarsson 和哈佛药学院的 Peter Kharchenko 。

这篇文章主要是提出了一个 RNA velocity 的概念。通过标准单细胞测序数据测量得到mRNA剪切前后的比例来估计RNA丰度随时间的变化。作者认为这种变化代表了细胞状态的改变，是一种动态的对单细胞状态的观测。而寻常的RNA丰度分析手段并不能展现出一个动态的细胞状态变化的过程。

进一步，这个指标可以用于预测每个细胞当前状态的下一个状态（以小时为基本时间尺度）。
作者在神经嵴细胞系 (Neural crest lineage) 中验证了这一指标的准确性，在文章中展示了具体应用方式，重建了小鼠海马体 (mouse hippocampus) 的分化树 (branching lineage tree), 测试了人类胚胎脑部的RNA变化。
作者希望这个指标可以用于协助分析和揭示人类细胞的谱系发育和细胞内的动态变化。

Preface

Thanks to this blog, I learned to enble MathJax equation numbering in my blog.

However, when I tried to write down equations, it’s so confusing that whether I write down the things I want, and it always takes too much time for trial and error. So I decided to record the trials for future references.

Preface

了解一下目前学术界对于某个基因在不同条件下使用不同transcripts这个概念的定义、了解程度和研究内容。

Preface

最近Genome Biology发了一个基于python的单细胞分析工具，针对目前越来越大的单细胞数据进行了优化，速度很快。
所以尝试用conda安装看看，方便管理环境。

文章链接：SCANPY: large-scale single-cell gene expression data analysis

Github: Scanpy – Single-Cell Analysis in Python

前言

精读一下文章, 记录一些东西，其实好像就是翻译一下。

今天的主角是这篇Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs，发表在Nature Communication杂志上，是日本理化研究所（RIEKN）的成果。
这篇文章主要介绍了他们建立的RamDA-seq测序方法，号称是第一个针对单细胞的全长总RNA组测序方法。

Introduction

git is a very useful and powerful tool for version control and team work. It’s commonly used in computer field, but it can be useful in the work of other fields too. I’ve been used it through package developing using Rstudio for a while. Recently, in order to auto-update this blog, I’ve learned some useful git skills. That’s the moment I want to write all I’ve learned so far down as a memo as usual and try to keep up.

The idea that use Travis CI to autoupdate GitHub pages is based on a post of IIssNan who also built NexT, the great theme that I am using.

Link to the original: http://notes.iissnan.com/2016/publishing-github-pages-with-travis-ci/

Introduction

Again, KevinZ recommond this autoupdating method to me. And for better understanding and future use, I decided to write the whole process down in my own way.
Auto-updating enables you to build your blog without setting up the entire environment in a new computer. All you need to do is pull your repo back, change it, and then push it back. That simplify the posting process if you have to work in multiple locations.

Introduction

I am working on a README file for a project recently. These files are commonly written by MarkDown. However, I can’t help noticing that some documentations contain hyperlinks which act as index. So I tried to figure out how to add TOC(Table Of Contents) in a Markdown file.