Python: Query reference sequences using rpy2 and BSgenome
Usually this job is done in R, as deescribed in Using R + Bioconductor to Get Flanking Sequence Given Genomic Coordinates. An R sample could be this simple:
Recent Posts
Python: List multiplication is actually repetition
之前遇到过这么一个例子：
Python: Iterating a file by every 2 lines
一个有点鸡贼的方法：
Handy Python Profiler: line_profiler + kernprof
Just take a look at an exemplar output and you’ll know what they are designed for.
Binary Encoding vs One hot Encoding
需要注意的是：one-hot encoding 应该是 binary encoding 的特殊情况。one-hot 的意思就是：只有一个 bit 是高位（1）；类似还有 one-cold encoding
Digest of Information Theory, Inference, and Learning Algorithms
1. Introduction to Information Theory
CPU bound vs IO bound
From stackoverflow: What do the terms “CPU bound” and “I/O bound” mean?:
Digest of Essence of Linear Algebra
Greatest thanks to 3Blue1Brown!
Building GWAVA environment on Ubuntu 16.04
GWAVA, Genome Wide Annotation of VAriants, is a tool aiming to predict the functional impact of non-coding genetic variants. It consists of two parts: