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Clonality of two types of somatic events are estimated in CHAT: somatic copy number alteration (s CNA) and somatic mutation. Data Preparation Before analysis, make sure you have access to two types of data for each tumor/normal pair to complete the full pipeline: allele specific SNP array and DNA sequencing data.To note, the first step of CHAT pipeline is to estimate s AGP using SNP array data, so if sequencing data is not available, users can still estimate s AGP.

We’re only, just now, beginning to make a legitimate impact. And now it’s all being wrested from us, halted by a slew of suits who believe they know what’s best. They’re the ones, after all, who’ve compiled both numbers and stories. * * * Before arriving last March we’d read that Kazakhstan maintained a manageable and enviable stability, serving as an oasis of tranquility among its besieged neighbors.

They know how many of us have been attacked and assaulted – according to our Country Director, Kazakhstan has earned the highest rate of any country in Peace Corps – and they know exactly what pressures have begun emanating from oblast- and national-level governments. It stood out among the ‘stans for its balance of temerity and growth, for its ability to manage disparate populations and divergent neighbors.

Below is a detailed instruction of usage of the R package CHAT (also available as CRAN-R package).

This tool is designed to systematically analyze tumor subclonality using SNP array and DNA sequencing data from tumor/normal pair samples.

The voice on the other end of the line, a voice tired and scratchy from relaying the days’ news to countless volunteers sequestered in North Kazakhstan, told me that after 18 years of work, Peace Corps would no longer be serving Kazakhstan. As it is, we’re departing only eight months into a 27-month commitment. We’ve just finished our second round of trainings, learning how to parse grant options and further implement community projects.

On Wednesday afternoon, standing coat-less in a soft snowfall, I learned that I would be forced to leave Kazakhstan in but a handful of days. Language skills are only just sticking, and our teaching impacts are only just sinking in.

Watch a Human Rights Watch report on the extortion and torture of gay men by Kazakh police, AFTER THE JUMP…

In the year since the vanishing of MH370, I appeared on CNN more than 50 times, watched my spouse’s eyes glaze over at dinner, and fell in with a group of borderline-obsessive amateur aviation sleuths. In the year since the vanishing of MH370, I appeared on CNN more than 50 times, watched my spouse’s eyes glaze over at dinner, and fell in with a group of borderline-obsessive amateur aviation sleuths. The unsettling oddness was there from the first moment, on March 8, when Malaysia Airlines announced that a plane from Kuala Lumpur bound for Beijing, Flight 370, had disappeared over the South China Sea in the middle of the night.

Allele-specific SNP array data contains two types of signals for each SNP: intensity of A allele and intensity of B allele. In CHAT, the input is commonly used log R ratio (LRR) and B-allele frequency (BAF), transformed from the original intensities: LRR = log2(intensity of A B)-1 BAF = intensity of B / intensity of (A B) The pipeline is optimized using SNP array data of both Illumina and Affymetrix platforms.

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