tophat | Spliced read mapper for RNA-Seq | Genomics library

 by   DaehwanKimLab C++ Version: Current License: BSL-1.0

kandi X-RAY | tophat Summary

kandi X-RAY | tophat Summary

tophat is a C++ library typically used in Artificial Intelligence, Genomics applications. tophat has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat2 (the current release) is a collaborative effort between the Center for Computational Biology at Johns Hopkins University and the Genome Sciences Department at the University of Washington. Please see for more information.
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              tophat has a low active ecosystem.
              It has 87 star(s) with 43 fork(s). There are 18 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 35 open issues and 11 have been closed. On average issues are closed in 57 days. There are 2 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of tophat is current.

            kandi-Quality Quality

              tophat has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              tophat is licensed under the BSL-1.0 License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              tophat releases are not available. You will need to build from source code and install.

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            tophat Key Features

            No Key Features are available at this moment for tophat.

            tophat Examples and Code Snippets

            No Code Snippets are available at this moment for tophat.

            Community Discussions

            QUESTION

            How to select correct contour the group of six digits
            Asked 2021-Jun-03 at 17:09

            I have a batch of screenshots like here:

            and I try to detect the region with six digits and recognize them. The second part works like a charm. I have a problem detecting the correct region because it can be placed with a shift depending on screen dimensions. For example, crop image looks like this:

            Seems it looks ok, but I have to add some workaround in code to select the right place.

            My code:

            ...

            ANSWER

            Answered 2021-Jun-03 at 17:09

            There are no magics in software...

            Inappropriate filters "eats" part of your digits.

            • Remove the tophat filter.
            • Remove the Sobel filter.
            • Replace cv2.THRESH_BINARY with cv2.THRESH_BINARY_INV.
            • Increase the size of sqKernel.

            I recommend you to draw the contours, and show (or save) intermediate results for testing.

            Here is the modified code:

            Source https://stackoverflow.com/questions/67823572

            QUESTION

            Not sure what is causing the error "Tuple index out of range"
            Asked 2021-Mar-06 at 12:47

            I am trying to answer this question: Create a function cubefit(xdata, ydata) (arguments in that order) that returns a numpy array of the best fit* parameters [A, B, C, D] that fit the list xdata of x values to the list ydata of y values, to a cubic equation of the form y= Ax^3 + B x^2 + C x + D

            *where the fit is determined using a non-linear least-squares regression test (the default fit method of scipy's curve_fit() function)

            This is my attempt:

            ...

            ANSWER

            Answered 2021-Mar-06 at 12:47

            If you read the scipy.optimize.curve_fit() documentation, you'll see what is happening:

            Returns

            • popt: array

              Optimal values for the parameters so that the sum of the squared residuals of f(xdata, *popt) - ydata is minimized.

            • pcov: 2-D array

              The estimated covariance of popt. The diagonals provide the variance of the parameter estimate. To compute one standard deviation errors on the parameters use perr = np.sqrt(np.diag(pcov)). [...]

            The function returns two results, both arrays. When you look further down, in the examples section, you see how the authors think you should use the function:

            Source https://stackoverflow.com/questions/66505513

            QUESTION

            Animation of the image of the WINTER BASH 2020 season
            Asked 2021-Jan-06 at 12:15

            WINTER BASH 2020 season is coming to an end, and I thought it would be instructive to figure out the CSS and other markup for generating the excellent logo shown here:

            In the image below, the numbers indicate the desired objects for animation

            Animation script:

            1. Hat generator. Should move unevenly up and down

            2. The question mark should float in space with a simultaneous change in size. What does the collection of information about the disclosure of the conditions for obtaining "secret hats" symbolize.

            3. The balloon should wiggle evenly.

            4. The small blue hat should move along the path of the word WINTER

            5. Moon wiggle. Should start after completing point 4 of the scenario

            6. The big blue hat moves forward in search of new hats. Some time after the start of step 6, hats should begin to fall from above.

            7. Animation of stars, should start after finding all the hats.

            I managed to implement the first point of the scenario.

            Hat animation starts after clicking on the canvas

            ...

            ANSWER

            Answered 2021-Jan-04 at 14:55

            LIVE DEMO

            The code turned out to be quite large, to place it in a snippet with a limit of 30,000 characters, I had to optimize it quite a lot and get rid of some embellishments.
            Comments remained on the main points of the program, I hope they will help you understand, if there is a need, I will make an additional answer with detailed explanations of the animation elements. The animation will start after clicking the Start button

            The music track sounds: Candy Dulfer / Dave Stewart - Lily Was Here

            Source https://stackoverflow.com/questions/65560112

            QUESTION

            Image goes black after thresholding
            Asked 2020-Jul-27 at 21:30

            I am trying to extract blood network from this face image: Face image

            For such task, i am using the P&M anisotropic diffusion found in this question: Anisotropic diffusion 2d images. Then i am using tophat transform followed by blackhat transform, afterwards i use a simple threshold to set to 255 all pixel that has an intensity value of 100.

            The problem is that, after i use the threshold and try to open the image, whatever way i try, the image is displayed as fully black:

            In short, my goal is to extract the blood vessels using P&M anisotropic diffusion with structuring element of flat disk of 5x5, then apply tophat and blackhat, respectively and a simple threshold and actually be able to view the image afterwards.

            Here's my code on how i am trying it:

            ...

            ANSWER

            Answered 2020-Jul-27 at 21:30

            I executed a simple MATLAB implementation, and got a nice result.

            MATLAB code:

            Source https://stackoverflow.com/questions/63043398

            QUESTION

            How to get the sum out of my switch in Swift?
            Asked 2020-Apr-20 at 02:30

            Hi I'm stuck trying to solve this: class Classy, to represent how classy someone or something is. "Classy". If you add fancy-looking items, "classiness" increases!

            Create a method, addItem() in Classy that takes a string as input, adds it to the "items" array and updates the classiness total.

            Add another method, getClassiness() that returns the "classiness" value based on the items.

            The following items have classiness points associated with them:

            1. "tophat" = 2
            2. "bowtie" = 4
            3. "monocle" = 5

            Everything else has 0 points.

            The sum is not performing correctly. The first problem is when it falls in te default case, everything is 0, I've tried in the default with:

            ...

            ANSWER

            Answered 2020-Apr-20 at 02:30

            Your switch case need update, it need to loop and the case is String not Array

            Source https://stackoverflow.com/questions/61312609

            QUESTION

            HTML: JQuery Every selected image appears in same container
            Asked 2020-Apr-18 at 23:00

            So basically I'm not a web developer and I really don't know how to talk about this issue correctly. So I'm building an arrow selector which has many selection fields and I have a div with pictures, the pictures changes within a user-selected field, so right here I have some bugs which appear when the user tries to select some options. For example, if I would select one field of arrow color, the image in the div changes, but in the wrong container( Every selected image appears in same container )

            My Selector BUG GIF example:

            The website with the selector which is functions well, you can see that every select option works good with the image.

            My JQuery code:

            ...

            ANSWER

            Answered 2020-Apr-18 at 23:00

            Almost all of the images appear in the wrong container because according to this line in your script

            Source https://stackoverflow.com/questions/61297346

            QUESTION

            HTML: JQuery how to use JQuery to get data-dk-dropdown-value
            Asked 2020-Apr-18 at 14:27

            I'm trying to make selection options and I need to change the class of selected item which is selected (On mouse over), so basically I'm not a web-developer so I really don't know how to achieve this, I was trying to research for this, but I didn't succeed.

            So I need two things, once the user mouse over the selected opinion the class of li changes to dk_option_current and once the user clicks on the selection I can do some future stuff, I really don't know how to achieve this, I may be using Javascript, but that's just a lot of work to do my myself.

            ...

            ANSWER

            Answered 2020-Apr-18 at 14:27

            It you really would prefer to use mouseover instead of using CSS :hover you can do it like this:

            Source https://stackoverflow.com/questions/61290388

            QUESTION

            Head First Java Problem- Main method not found
            Asked 2019-Dec-15 at 17:46

            I have trawled through the internet for a solution to this and I still don't understand why I am getting the following error message:

            "Error: Main method not found in class DrumKit, please define the main method as: public static void main(String[] args) or a JavaFX application class must extend javafx.application.Application"

            Here is my code:

            DrumKit.java

            ...

            ANSWER

            Answered 2019-Dec-15 at 16:15

            Your class containing the main method must be public

            Source https://stackoverflow.com/questions/59345602

            QUESTION

            Python: How to get the convolution of two continuous distributions?
            Asked 2019-Dec-09 at 22:12

            Let X, Y be 2 random variables, with probability density functions pdf1 and pdf2.

            Z = X + Y

            Then the probability density function of Z is given by the convolution of pdf1 and pdf2. Since we can't deal with continuous distributions, we descritize the continuous distributions and deal with them.

            To find the convolution of uniform distribution and normal distribution, I came up with following code.

            ...

            ANSWER

            Answered 2018-Sep-17 at 06:25

            To make this work with discretized pdf's you need to normalize the output of fftconvolve:

            Source https://stackoverflow.com/questions/52353759

            QUESTION

            How to normalize kde of scikit learn?
            Asked 2019-Aug-09 at 15:39

            Let's say I have an array of shape (100000,1), representing samples of variable X of uniform distribution between 0 and 1. I want to approximate the density of probability of this variable, and I use Scikit-Learn KernelDensity to do that.

            The problem is I only get a result which is not normalized. The integral of probability density does not sum to 1. How should I do to normalize automatically ? Am I doing something wrong ?

            ...

            ANSWER

            Answered 2019-Aug-09 at 14:24

            these are probabilities at each point - what will happen if

            X1 = np.linspace(0,1,10000000)[:,np.newaxis]

            ?

            array you get is not distribution/sample from random variable

            Source https://stackoverflow.com/questions/57431332

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

            Vulnerabilities

            No vulnerabilities reported

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            You can download it from GitHub.

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