On the Subtyping of Cancers

Mes, Pro, and Meta.

proliferative ki-67

http://en.wikipedia.org/wiki/Ki-67_(protein)

The Ki-67 protein (also known as MKI67) is a cellular marker for proliferation.^[5] It is strictly associated with cell proliferation. During interphase, the Ki-67 antigen can be exclusively detected within the cell nucleus, whereas in mitosis most of the protein is relocated to the surface of the chromosomes. Ki-67 protein is present during all active phases of the cell cycle (G₁, S, G₂, and mitosis), but is absent from resting cells (G₀).

My paper is highlighted by Gastroenterology Editorial

My paper, "Identification of molecular subtypes of gastric cancer with different responses to PI3-kinase inhibitors and 5-fluorouracil",
http://www.sciencedirect.com/science/article/pii/S0016508513007221
is highlighted by Gastroenterology Editorial:

Expanding the Lauren Classification: A New Gastric Cancer Subtype?
http://www.sciencedirect.com/science/article/pii/S0016508513010706
https://dl.dropboxusercontent.com/u/62547840/GastroenterologyEditorial.pdf

Extract specific rows from a file

 cat CCI_DrugFile_trimmed.csv |  awk ' NR >= 297652 && NR <= 298124 {print }'>row297652to298124.txt

install python package "poster"

It's quite simple, you can use easy_install or pip, in your terminal run:

easy_install poster

or

pip install poster

If you don't have easy_install or pip, install distribute first:

curl -O http://python-distribute.org/distribute_setup.py
python distribute_setup.py

I recommend using pip and reading the excellent documentation. You might also benefit from reading the python documentation about distributing modules.

In the future search pypi. If it's on pypi you can pip or easy_install it.

reference:

http://stackoverflow.com/questions/5906878/installing-posterstreaming-http-uploads-and-multipart-form-data-encoding

nohup scp ... &

scp as a background process
To execute any linux command in background we use nohup as follows:

$ nohup SOME_COMMAND &
But the problem with scp command is that it prompts for the password (if password authentication is used).
So to make scp execute as a background process do this:

$ nohup scp file_to_copy user@server:/path/to/copy/the/file > nohup.out 2>&1
Then press ctrl + z which will temporarily suspend the command, then enter the command:

$ bg
This will start executing the command in backgroud

mapping rates from BWA

You can run bamtools stats -in path/to/your/alignments.bam, which will (quickly) report general alignment statistics.

You can also run bamtools filter -isMapped false -in path/to/your/alignments.bam > unmapped.bam (or something quite close to that) to get your unmapped reads.

http://www.biostars.org/p/10763/

you can tell from the sam file, by checking the flags, or make the file into a .bam with samtools, and use flagstat from samtools to count.