SigMA | Mutational signature analysis for low statistics SNV data | Analytics library

by parklab R Version: 2.0 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | SigMA Summary

SigMA is a R library typically used in Analytics applications. SigMA has no bugs, it has no vulnerabilities and it has low support. However SigMA has a Non-SPDX License. You can download it from GitHub.

Copyright (c) 2019 - President and Fellows of Harvard College. All rights reserved.

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SigMA has a low active ecosystem.

It has 55 star(s) with 21 fork(s). There are 6 watchers for this library.

It had no major release in the last 12 months.

There are 2 open issues and 24 have been closed. On average issues are closed in 189 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of SigMA is 2.0

Quality

SigMA has no bugs reported.

Security

SigMA has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

SigMA has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

SigMA releases are available to install and integrate.

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SigMA Key Features

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SigMA Examples and Code Snippets

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Community Discussions

Trending Discussions on SigMA

Can't integrate simple normal distribution in sympy, depending on mean and deviation constants

Trying to blur highest variance point of an image but some conversion problem exist in code

How can I avoid a loop if I need to do a matrix multiplication?

Sympy.solve provides "AttributeError"

Calculation of the first and third quartile

Min and Max across multiple columns with NAs

one component Gaussian fit with python is not working

pyglet gives error regarding GLSL version

R - Apply function to list of lm summaries

Sum weighted Rayleigh distribution

QUESTION

Can't integrate simple normal distribution in sympy, depending on mean and deviation constants

Asked 2021-Jun-15 at 19:02

So... I can sympy.integrate a normal distribution with mean and standard deviation:

...

ANSWER

Answered 2021-Jun-15 at 01:38

Here's a close case that works:

Source https://stackoverflow.com/questions/67978829

QUESTION

Trying to blur highest variance point of an image but some conversion problem exist in code

Asked 2021-Jun-10 at 20:29

I am trying to blur of highest variance point from the image. I wrote code below. 1st part finds the variance of the image. I checked the resultant variance of an image and it is correct. (I used Lena's image) In 2nd part, I find the highest variance coordinates and send to this Function which finds gaussian blur. When I execute this code, it throws "C:\Tmp\blur_highest_variance.py", line 66, in sigma=15) numpy.core._exceptions.UFuncTypeError: Cannot cast ufunc 'subtract' output from dtype('float64') to dtype('uint8') with casting rule 'same_kind' I tried a few conversions between types but no avail. Can you show me some direction?

...

ANSWER

Answered 2021-Jun-10 at 18:48

The error message tells us the line and the reason for the error:

Traceback (most recent call last):
File "C:\Tmp\blur_highest_variance.py", line 66, in sigma=15)
numpy.core._exceptions.UFuncTypeError: Cannot cast ufunc 'subtract' output from dtype('float64') to dtype('uint8') with casting rule 'same_kind'

It is more simple to debug the code using intermediate variables:
For example, use an intermediate named gmask:

Source https://stackoverflow.com/questions/67924044

QUESTION

How can I avoid a loop if I need to do a matrix multiplication?

Asked 2021-Jun-10 at 11:49

I have the following code:

...

ANSWER

Answered 2021-Jun-10 at 00:41

I believe this will work:

Source https://stackoverflow.com/questions/67907491

QUESTION

Sympy.solve provides "AttributeError"

Asked 2021-Jun-09 at 19:36

If sigma[i, j] == 0 or sigma[i, j] == 1 it doesnt matter. It only takes the position of non-zero elements. There is a code that provides finding coeffs y1, y2, w1, w2, which are sympy.symbols, of func f by sympy.solve. C - is a matrix.

The process of creating C-matrix:

...

ANSWER

Answered 2021-Jun-09 at 19:36

Since you weren't providing the information I asked for, I tried to write a small test case, seeking to get at the core of your problem.

Mixing numpy and sympy is tricky and somewhat unpredictable. But sometimes sympy symbols can be used in numpy expressions.

Source https://stackoverflow.com/questions/67909623

QUESTION

Calculation of the first and third quartile

Asked 2021-Jun-09 at 14:05

I'm trying to calculate the mean, standard deviation, median, first quartile and third quartile of the lognormal distribution that I fit to my histogram. So far I've only been able to calculate the mean, standard deviation and median, based on the formulas I found on Wikipedia, but I don't know how to calculate the first quartile and the third quartile. How could I calculate in Python the first quartile and the third quartile, based on the lognormal distribution?

...

ANSWER

Answered 2021-Jun-08 at 20:07

Given a log-normal distribution, we want to compute its quantiles. Furthermore, the parameters of the log-normal distribution are estimated from data.

The script below uses OpenTURNS to create the distribution using the LogNormal class. It takes as inputs arguments the mean and standard deviation of the underlying normal distribution. Then we can use the computeQuantile()method to compute the quantiles.

Source https://stackoverflow.com/questions/67886115

QUESTION

Min and Max across multiple columns with NAs

Asked 2021-Jun-08 at 11:55

For the following sample data dat, is there a way to calculate min and max while handling NAs. My input is:

...

ANSWER

Answered 2021-Jun-08 at 11:12

The following solution seems to work with the transform() function:

Source https://stackoverflow.com/questions/67885771

QUESTION

one component Gaussian fit with python is not working

Asked 2021-Jun-08 at 07:34

i have the orange peak that I want to do a Gaussian fit on with the aim of obtaining an estimate of the FWHM and the maximum temperature:

The function is given by:

...

ANSWER

Answered 2021-Jun-08 at 07:34

The typical reason for the fail is: wrong starting parameters. The formulae used here are somewhat those that would be used for a measurement statistic, while the data here has to be considered the according histogram. The use of n, hence, does not make sense. It is more like

Source https://stackoverflow.com/questions/67836870

QUESTION

pyglet gives error regarding GLSL version

Asked 2021-Jun-08 at 07:05

I am trying to run a code that has a GUI built with pyglet. but it gives this error. I have searched and found that I need to directly set the version of GLSL to be used by the code but I don't know how. would be happy if you helped me out with it.

...

ANSWER

Answered 2021-Jun-08 at 07:05

well it got solved! just needed to add the directive #version 120 at the beginning of the shader like this:

Source https://stackoverflow.com/questions/67856810

QUESTION

R - Apply function to list of lm summaries

Asked 2021-Jun-07 at 17:41

I have a list with the summaries of different linear regressions. I want to extract the coefficients and p-values of all the elements of the linear regressions and put them in a dataframe (one dataframe per each element of the lm).

For example, to extract the coeffcients of the interecpt I am using the follwing:

...

ANSWER

Answered 2021-Jun-07 at 03:10

Change your function to -

Source https://stackoverflow.com/questions/67864253

QUESTION

Sum weighted Rayleigh distribution

Asked 2021-Jun-07 at 12:17

I simulated data with nrow=1000 (individuals) and ncol=100 (days) for step lengths according to a Pareto distribution function:

...

ANSWER

Answered 2021-Jun-07 at 12:17

First, it looks like you have an error in your Rayleigh PDF. It should be:

Source https://stackoverflow.com/questions/67605521

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install SigMA

You can download it from GitHub.

Support

Requests for use of the Software for or on behalf of for-profit entities or for any commercial purposes, please contact:. Office of Technology Development Harvard University Smith Campus Center, Suite 727E 1350 Massachusetts Avenue Cambridge, MA 02138 USA Telephone: (617) 495-3067 E-mail: otd@harvard.edu.

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