Posts Tagged ‘stl’

Timing, rates and spectra of human germline mutation : Nature Genetics : Nature Publishing Group

May 17, 2016

Timing, rates & spectra of human germline mutation Metaanalysis of >6500 events gives a de novo mutational signature

PLOS Genetics: A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures

February 27, 2016

Model-Based Approach to Inferring…#Cancer Mutation Signatures Assuming independence betw 3 NTs, 11 v 95 parameters

The first contribution of this paper is to suggest a more parsimonious approach to modelling mutation signatures, with the benefit of producing both more stable estimates and more easily interpretable signatures. In brief, we substantially reduce the number of parameters per signature by breaking each mutation pattern into “features”, and assuming independence across mutation features. For example, consider the case where a mutation pattern is defined by the substitution and its two flanking bases. We break this into three features
(substitution, 3′ base, 5′ base), and characterize each mutation signature by a probability distribution for each feature (which, by our independence assumption, are multiplied together to define a distribution on mutation patterns). Since the number of possible values for each feature is 6, 4, and 4 respectively this requires 5 + 3 + 3 = 11 parameters instead of 96 − 1 = 95 parameters. Furthermore, extending this model to account for ±n neighboring bases requires only 5 + 6nparameters instead of 6 × 42n − 1. For example, considering ±2 positions requires 17 parameters instead of 1,535. Finally,
incorporating transcription strand as an additional feature adds just one parameter, instead of doubling the number of parameters. “}}

Identification of neutral tumor evolution across cancer types : Nature Genetics : Nature Publishing Group

February 27, 2016

Neutral tumor #evolution across #cancer types Initial burst of driver events followed by random mutations

H1B visa statistics

July 23, 2015

1000 or 1024

June 26, 2015

KiB v kb, 1024 v 1000. Appears powers of 10 win out over powers of 2

how to get full path of a unix file

September 6, 2014


1. Drag the file from finder to a terminal. Yes, pull it out with some effort and just drop it right there…

2. The full path will magically show up in no time!

ON LINUX According to Stackoverflow, you should do:

readlink -f file.txt


find $PWD -iname “*” -maxdepth 1

find $PWD -maxdepth 1

Calendar exporter

August 14, 2014

calendar exporter:

It is simple but does the work you need: calendar exporting, event filter based on keywords and simple statistics.

chinese cancer data

July 18, 2014

Annotated somatic variants and interactive variant analysis results are available online

Eighty-eight primary HCC tumors and matched adjacent nontumor liver tissues were analyzed by whole-genome DNA sequencing to identify somatic mutations and HBV integration sites. The vast majority (92%,n = 81) of patients in this cohort were HBV carriers (i.e., HBsAg seropositive) suffering from chronic hepatitis B or cirrhosis. None of the patients were hepatitis C virus (HCV) positive

the data:

The original paper is here:

Guide to cancer genomics

January 17, 2014