Auto complete is good, it can save you times in typing and prevent typo sometimes.
RStudio now supports function arguments in auto complete. ESS’s auto complete is more advance, it supports help page.
We should use ‘ess-use-auto-complete’ to activate auto complete in ESS buffers.
(setq ess-use-auto-complete t)
The effect is quite amazing. Auto-complete extension is needed for ESS, we need to install the auto-complete extension and load it at Emacs startup.
One day, I am looking for R packages that can analyze PPI and after searching, I found the ppiPre package in CRAN.
Installing OS is painful, you need to re-install all the software and configure them to the way you want. We don’t want to wast time in doing this. To prevent doing this dirty job, we perform an upgrade install instead of clean install. We all have experience of upgrading Windows sucks, same as OS X. All the issues you have in old system will be remained, and sometimes new issues will be introduced in the process of upgrading. The system will be slower compare to clean install one.
The SIR model divides the population to three compartments: Susceptible, Infected and Recovered. If the disease dynamic fits the SIR model, then the flow of individuals is one direction from the susceptible group to infected group and then to the recovered group. All individuals are assumed to be identical in terms of their susceptibility to infection, infectiousness if infected and mixing behaviour associated with disease transmission.
We defined: $S_t$ = the number of susceptible individuals at time t
$ I_t $ = the number of infected individuals at time t
$R_t$ = the number of recovered individuals at time t
Suppose on average every infected individual will contact $\gamma$ person, and $\kappa$ percent of these $\gamma$ person will be infected. Then on average there are $\beta = \gamma \times \kappa$ person will be infected an infected individual.
Nearest gene annotation
Almost all annotation software calculate the distance of a peak to the nearest TSS and assign the peak to that gene. This can be misleading, as binding sites might be located between two start sites of different genes or hit different genes which have the same TSS location in the genome.
The function annotatePeak provides option to assign genes with a max distance cutoff and all genes within this distance were reported for each peak.
Usually Roche’s installer is a catastrophe, they only provides rpm packages of the software for 454 GS FLX (version 2.9). Although the package contains setup.sh, the script is useless since it is actually a binary payload.
I run the setup.sh, and it throw error of not finding /sbin/lspci. In debian derived distribution, lspci command is located in /bin folder. This issue is easy to solve by adding a soft link to /sbin/lspci.
在进行测序的时候，需要将DNA打断，构建library，这些fragment需要接上adaptor，好进行扩增，illumina的测序，可以有single end和paired end两种，分别从一端和两端进行测序。
fragment ========================================
fragment + adaptors ~~~========================================~~~
SE read --------->
PE reads R1---------> <---------R2
unknown gap ....................
