Just some basic notations
Derivative $$ f^{\prime} (x) = \frac {df(x)} {dx} $$
Gradient Generalize the derivative to the multivariate functions.
The first order derivative of a multivariate functions.
$$ \nabla f=\left[\frac{\partial f\left(x_{1}, x_{2}, x_{3}\right)}{\partial x_{1}}, \frac{\partial f\left(x_{1}, x_{2}, x_{3}\right)}{\partial x_{2}}, \frac{\partial f\left(x_{1}, x_{2}, x_{3}\right)}{\partial x_{3}}\right] $$
Jacobian a generalization of the derivate operator to the vector-valued functions
Maximum Likelihood Estimation Gaussian Mixture Model Expectation Maximization 1. Probability and likelihood likehood & maximum likehood 在非正式场合似然（likelihood）和概率（Probabilit
usefull tools for linux command line
Make terminal cool, install OhMyZsh 1 2 3 4 5 6 7 8 # install zsh sudo apt-get install zsh # ubuntu # change default shell to zsh chsh -s /usr/bin/zsh # install ohmyzsh sh -c "$(wget https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh -O -)" source ~/.zshrc ssh login withoutpassword on your local machine, run 1 ssh-keygen press Enter 3 time until finished.
hisat2-htseq-deseq2
3.1 transcriptom mapping step 0: install tools
1 conda install htseq hisat2 stringtie step 1: build index and extract splice sites
build index
1 2 hisat2-build -p {threads} genome/hg38.fa hisat2_index/hg38 extract known splice sites for alignmnet
1 2 hisat2_extract_splice_sites.py gencode.gtf > hisat2_index/splicesites.txt hisat2_extract_exons.
bowtie2-macs2-deeptools
2.1 Genome mapping Step 0: install software
1 2 # install miniconda, then call conda conda install -c bioconda bowtie2 hisat2 samtools deeptools step 1: build index
1 bowtie2-build hg38.fa bowtie2_index/hg38 step 2: mapping
Unpaired data
1 2 3 bowtie2 -p ${threads} -x index/hg38 \ -U input.
salmon-tximport-deseq2
Step 0: install salmon and download transcriptome cdna from gencode 1 2 conda install salmon wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.transcripts.fa.gz Step 1. build salmon index 1 salmon index -p 8 --gencode -t gencode.v32.transcripts.fa.gz -i salmonIndex_hg38 Step 2: quantification 1 2 3 4 salmon quant -i salmonIndex_hg38 -l A \ -1 ${fn}/${samp}_1.
