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Hi, there

Derivative, Gradient, Jacobian, Hessian, Laplacian

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

Shortcut to bulk RNA-seq analysis

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.

SuperFast RNA-seq

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.