splatter | Simple simulation of single-cell RNA sequencing data | Genomics library

 by   Oshlack R Version: v1.22.0 License: GPL-3.0

kandi X-RAY | splatter Summary

kandi X-RAY | splatter Summary

splatter is a R library typically used in Artificial Intelligence, Genomics applications. splatter has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Splatter is an R package for the simple simulation of single-cell RNA sequencing data. Splatter provides a common interface to multiple simulations that have:. Splatter is built on top of scater and stores simulations in SingleCellExperiment objects. Splatter also has functions for comparing simulations and real datasets.
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              splatter has a low active ecosystem.
              It has 178 star(s) with 52 fork(s). There are 6 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 9 open issues and 130 have been closed. On average issues are closed in 37 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of splatter is v1.22.0

            kandi-Quality Quality

              splatter has 0 bugs and 0 code smells.

            kandi-Security Security

              splatter has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              splatter code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              splatter is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              splatter releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.
              It has 8 lines of code, 0 functions and 1 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

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            splatter Key Features

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            splatter Examples and Code Snippets

            No Code Snippets are available at this moment for splatter.

            Community Discussions

            QUESTION

            To what does a 2D array points to?
            Asked 2021-Oct-10 at 15:11

            That's might be a dumb question, but I was reading a book and they splattered to me this code

            ...

            ANSWER

            Answered 2021-Oct-10 at 01:25

            An array, whether one-dimensional, two-dimensional, or more, does not point to anything. It is a set of objects of the same type in contiguous memory.

            After int arr[6][8];, arr is an array of 6 arrays of 8 int. If each int uses four bytes, then the entire array uses 6•8•4 = 192 bytes in memory, and sizeof arr will evaluate to 192, because arr is the array, and sizeof gives the size of its operand.

            When you use arr in an expression, it will be automatically converted to a pointer to its first element, except when it is the operand of sizeof or of unary &.1 Because arr is an array of arrays, its first element is also an array. The first element of arr is arr[0], which is an array of 8 int. So, in arr+1, arr is converted to a pointer to its first element. That pointer is &arr[0], the address of arr[0].

            When an integer, say n is added to a pointer, the result points to n further elements long in the array. So, when we add 1 to &arr[0], we get &arr[1]. Thus, in arr+1, arr is automatically converted to &arr[0], producing &arr[0]+1, and then the addition produces &arr[1].

            Thus, arr+1 is &arr[1], which is also the place where arr[1][0] is. (Note that while &arr[1] and &arr[1][0] point to the same place in memory, they have different types, so the compiler treats them differently when doing arithmetic with them.)

            After int *ptr = &arr[0][0];, ptr of course points to arr[0][0]. Then ptr+8 points to where arr[0][8] would be if there were such an element. Of course, there is no, since arr[0] has only elements from arr[0][0] to arr[0][7]. ptr+8 points one beyond arr[0][7].

            That pointer arithmetic is defined by the C standard; you are allowed to point “one beyond the last element.” However, that is only a placeholder pointer, useful for arithmetic and comparisons. The C standard does not happen when you dereference the pointer, with *(ptr+8).

            We know that arr[1][0] is in the place where arr[0][8] hypothetically would be. However, the C standard does not give us rules that say we can definitely use *(ptr+8) to access arr[1][0]. So that code does not have behavior defined by the C standard. Many compilers will treat it has accessing arr[1][0], though.

            As you note, *(*(arr+1)) can be used to access arr[1][0]. The way this works is:

            • arr is automatically converted to &arr[0].
            • Adding 1 gives &arr[1].
            • * dereferences &arr[1], producing arr[1].
            • arr[1] is an array, so it is automatically converted to a pointer to its first element. This produces &arr[1][0].
            • * dereferences &arr[1][0], producing arr[1][0].

            In contrast, *(*(arr+8)) does not work to access arr[1][0]:

            • arr is automatically converted to &arr[0].
            • Adding 8 gives &arr[8].

            Now we are well beyond where arr ends. arr has only elements from arr[0] to arr[5], so arr[8] is beyond the end.

            Note that adding 8 to &arr[0] moved the pointer by 8 elements of the arr array, not by 8 eleemnts of the arr[0] array. That is, it moved it by 8 arrays of 8 int, not by 8 int. That is because the type of &arr[0] is “pointer to array of 8 int”, not “pointer to int”.

            When you add 8 to a “pointer to int”, you move it by 8 int. When you add 8 to a “pointer to an array of 8 int”, you move it by 8 arrays of 8 int.

            Footnote

            1 All arrays are automatically converted like this, and there is one more exception for string literals. When a string literal, which is an array of characters, is used to initialize a character array, it is not automatically converted to a pointer.

            Source https://stackoverflow.com/questions/69510967

            QUESTION

            Can't figure out to solve this image segmentation problem
            Asked 2020-Oct-17 at 22:10

            My training images are made up of blue channels extracted from the ELAs (Error Level Analysis) of some spliced images and the labels just consist their corresponding ground truth masks.

            I've have constructed a simple encoder-decoder CNN given down below to do the segmentation and have also tested it on the cell membrane segmentation task. There it performs well and creates near to ground truth images, so I guess the neural network I created is capable enough.

            However, it is not working on the spliced images on CASIA1 + CASIA1GroundTruth dataset. Please help me to fix it, I have spent too many days on it trying different architectures and pre-processing on the images but no luck.

            Input Image

            Ground Truth

            Output/Generated Image

            For one, it is claiming such high accuracy (98%) and low losses but the output image is so wrong. It is sort of getting the wanted mask if you look carefully but along with it there are a lot of regions splattered with white. Seems like it is not able to get the difference in the intensities of the pixels for the wanted region vs the background. Please help me fix it :(

            Preparation ...

            ANSWER

            Answered 2020-Oct-17 at 22:10

            Oops, I did a stupid one. In order to see what I have picked up for testing from the X array, I multiplied that array by 255 cause PIL doesn't display arrays in 0-1 range. Mistakenly, I just used the same modified variable and passed it in test/prediction.

            Source https://stackoverflow.com/questions/64400250

            QUESTION

            How to create the left to right or top to bottom overlay splattering animation in Flutter
            Asked 2020-Jun-20 at 04:41

            Unable to create the overlay splattering animation above the layout in flutter.

            ...

            ANSWER

            Answered 2020-Jun-19 at 07:42
            Added

            I updated code to look like attached gif.

            You can use 'AnimatedPositioned' Widget like below.

            Source https://stackoverflow.com/questions/62464471

            QUESTION

            Issue with Matplotlib rendering dates, image
            Asked 2020-Jun-01 at 11:40

            I'm having an issue with Matplotlib v 3.1.3 from conda-forge with python 3.7. I have all of the dependencies required for Matplotlib. When I enter this code, which should work. I get splatter art. It's based on this youtube tutorial: https://www.youtube.com/watch?v=LWjaAiKaf8&list=PL-osiE80TeTvipOqomVEeZ1HRrcEvtZB&index=8

            ...

            ANSWER

            Answered 2020-Jun-01 at 11:40

            It seems that the default setting in plot_date() is set to scatterplots (see (https://www.geeksforgeeks.org/matplotlib-pyplot-plot_date-in-python/) in the newer versions of matplotlib.

            To achieve a continuous graph based on dates, you can define the interlining in the arguments plt.plot_date(x_value, y_value, '-').

            This code works for me:

            Source https://stackoverflow.com/questions/62129895

            QUESTION

            How do I not have my table shift down when text lengths change? (Keep the table fixed in one position)
            Asked 2020-May-02 at 08:29

            I have a simple table set up with a generator above it that varies in text lengths. Every so often I get an extra line and that shifts my table down. Is there any way I could keep my table fixed in one position?

            Please ignore the Javascript and only look at CSS and HTML, specifically the sections related to ButtonSection and the Table. Thanks

            ...

            ANSWER

            Answered 2020-May-02 at 08:29

            You could try and wrap the text that varies in length in a div element and fix it's height, so that the longest text doesn't move the table.

            In your html:

            Source https://stackoverflow.com/questions/61551807

            QUESTION

            Fetching reddit data using praw into JSON Lines
            Asked 2020-May-01 at 15:25

            So I'm trying to fetch reddit posts data using praw and turn it into a JSON Lines file.

            What I need is something like this:

            ...

            ANSWER

            Answered 2020-May-01 at 15:25

            This is an interesting way to want to store the data. I can't say that I'd use this approach myself, since it involves duplicating the same information over and over again.

            To achieve this, you'll need to manage a stack containing the current context, and use recursion to get each comment's children:

            Source https://stackoverflow.com/questions/61544460

            QUESTION

            First Apache Server, Webpage Images Missing
            Asked 2020-Feb-26 at 00:25

            I just built my first AWS Apache Server and uploaded my website from my school project. The site works in Dreamweaver. However on my Apache server only some of the images appear. They all have the same path and are contained in the same folder /var/www/html/images. Some appear as intended, others are a broken link. Any ideas why it's not working? To get css to load I had to move my css folder. With the images some work fine while others do not. They are roughly the same size files. This is the code for one of the non working images:

            ...

            ANSWER

            Answered 2020-Feb-26 at 00:25

            I found that the file extension on some of the pictures was capitalized. These pictures wouldn't load until I changed .JPG to .jpg.

            Source https://stackoverflow.com/questions/60216988

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

            Vulnerabilities

            No vulnerabilities reported

            Install splatter

            Once installed the best place to get started is the vignette. For most users the most convenient way to access this is online here. To get started with population scale simulations, see the splatPop vignette here.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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