pique | efficient peak finder for high coverage ChIP

 by   ryneches Python Version: 0.1.7 License: No License

kandi X-RAY | pique Summary

kandi X-RAY | pique Summary

pique is a Python library typically used in Healthcare, Pharma, Life Sciences applications. pique has no bugs, it has no vulnerabilities, it has build file available and it has low support. You can install using 'pip install pique' or download it from GitLab, GitHub, PyPI.

The pique package is a high efficiency peak finder for ChIP-seq experiments that yield high coverage allignments to the reference genome. It was developed for studying gene expression in Halobacterium salinarum sp. NRC1, sequenced using barcoded 40bp Illumina reads as part of an ongoing project in Marc Facciotti's lab at UC Davis.
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            kandi-support Support

              pique has a low active ecosystem.
              It has 10 star(s) with 6 fork(s). There are 3 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 3 open issues and 4 have been closed. On average issues are closed in 10 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of pique is 0.1.7

            kandi-Quality Quality

              pique has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              pique does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              pique releases are not available. You will need to build from source code and install.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed pique and discovered the below as its top functions. This is intended to give you an instant insight into pique implemented functionality, and help decide if they suit your requirements.
            • Detect contigs
            • Find peaks for a given ARF
            • Apply filter
            • Calculate the noise threshold for a sample
            • Load Pique data
            • Add a contig
            • Find peak locations for a given ARF
            Get all kandi verified functions for this library.

            pique Key Features

            No Key Features are available at this moment for pique.

            pique Examples and Code Snippets

            No Code Snippets are available at this moment for pique.

            Community Discussions

            QUESTION

            Android LiveData<>> vs. List<> memory size comparison?
            Asked 2021-Apr-03 at 03:05

            So I've been reading more thoroughly into LiveData and my curiosity was piqued. LiveData can hold a list of anything, but how does that compare to a regular List in terms of memory allocation. I know generally it depends on what is being stored. A List can be larger than a List, if there's only 1 float and a 100 ints.

            But, for example, lets say I had a LiveData> of 10 phone numbers, and a List of the same phone numbers. Would the LiveData take up more memory?

            I know LiveData has a specific purpose in keeping the UI updated(I'm probably not articulating that accurately) and needs an Observer, whereas a plain List is easier to work with but can't meet the need LiveData fulfills.

            Or do most devices these days simply have enough memory that it's basically a moot point?

            ...

            ANSWER

            Answered 2021-Apr-03 at 03:05

            Would the LiveData take up more memory?

            For the same underlying list, yes. It's always going to occupy some space beyond the data it contains. Look at the source code to get a sense of what it actually adds on top of the contained data object.

            You're probably overthinking it. If you have a problem with running out of memory, it's almost certainly not because of any LiveData. Your list itself is likely the bigger issue, and other parts of the core Android runtime are going to dwarf the size of your LiveData and its contents.

            Source https://stackoverflow.com/questions/66927278

            QUESTION

            Python: Random trivia trivia question/answer, in parameters
            Asked 2021-Jan-21 at 14:59

            I am new to learning python and want to run bit of a trivia. Basically, I want to ask a random question from a list and then using an 'in' operator, figure if the user input of Y/N is correct or not. I'm stuck with determining how to check whether it is correct or not. Maybe my (incorrect) code can explain better.

            ...

            ANSWER

            Answered 2021-Jan-21 at 14:39

            Most importantly you have to save your random choice so you can verify it later. So you should asign two variables before:

            Source https://stackoverflow.com/questions/65829496

            QUESTION

            Concatting Strings Across Functions
            Asked 2020-Nov-02 at 17:32

            I'm working on a program that will take a text file and convert numbers from 0 - 99 to words (i.e 0 -> "zero", 99 -> "ninety nine"). I am able to convert the numbers and append them to the string within one function but the final sting output does not contain any of the converted numbers. Here is the code:

            ...

            ANSWER

            Answered 2020-Nov-02 at 17:32

            I can think of two ways of doing this:

            If you want to return the value of fullString to your main method, I suggest you modify convertToWord so that it has return type String, like this:

            Source https://stackoverflow.com/questions/64649549

            QUESTION

            Get section index of clicked element
            Asked 2020-Aug-17 at 18:14

            In my website I need to get the index of a clicked elements section.

            There is one

            with multiple and each one has a
              . Each sections has own, unique section headers.

              If you click a list element the class turns from listFUTItem has-auction-data to listFUTItem has-auction-data active (tried to rebuild that at the playground).

              At the

              only one list element can be active at once. (Not working at this snipped but at the website)

              At the moment my code works like this: itemList = document.querySelectorAll('.sectioned-item-list > ul')[2] But the index has to be variable.

              ...

            ANSWER

            Answered 2020-Aug-17 at 06:52

            Use closest() to traverse up to the

            and get it's index within the collection of all the sections of that class

            Source https://stackoverflow.com/questions/63445351

            QUESTION

            Decoding compiler output for interface run type assertion
            Asked 2020-Aug-13 at 15:46

            I recently encountered empty interfaces while using the Load() method of Atomic.Value . I was experimenting with empty interfaces type assertion a bit - https://play.golang.org/p/CLyY2y9-2VF

            This piqued my interest, and I decided to take a peek behind the curtains to see what actions does a compiler take so that the code doesn't panic in case of trying to read the concrete value on a nil interface {} (e.g., when you call Load.(type) when Store hasn't been called yet).

            I could see that in the unsafe version, compiler had this assembly instruction that cause the panic : call runtime.panicdottypeE(SB)

            The panic instruction is obviously not present in the safe version. Can someone please explain this in more details on what compiler is doing when we capture return value with ok (and perhaps point me to the corresponding assembly instructions in the godbolt link)?

            Here are the godbolt compiler links for unsafe version [1] and safe version [2].

            [1] https://godbolt.org/z/76onvj

            [2] https://godbolt.org/z/e8aoqe

            ...

            ANSWER

            Answered 2020-Aug-13 at 15:45

            The quick summary: they do exactly the same thing, it's just that the case for ok == false is different.

            The two bits have the following in common:

            Source https://stackoverflow.com/questions/63397922

            QUESTION

            How does Promise.resolve() work under the hood? Specifically, how exactly does it unwrap thenables?
            Asked 2020-Jun-28 at 12:23

            According to MDN:

            ...if the value is a thenable (i.e. has a "then" method), the returned promise will "follow" that thenable, adopting its eventual state;

            This piqued my interest a bit, so I wanted to see if it was possible to re-implement this functionality in pure Javascript. What I ended up with is this:

            ...

            ANSWER

            Answered 2020-Jun-28 at 12:23

            Promise.resolve does not rely on the return value of the .then() invocation on the thenable value. It rather looks similar to this:

            Source https://stackoverflow.com/questions/62621645

            QUESTION

            Get index of mutated Classname
            Asked 2020-May-15 at 12:48

            I got a list on a webpage.

            After I press a button the system changes the class from listFUTItem has-auction-data to listFUTItem has-auction-data won.

            I observe the list with a mutationobserver and want to get the index of the changed classelement.

            I got no idea of how to get the index at all.

            At the webpage you only can have ONE listFUTItem has-auction-data wonat once. I didnt know how to toggle it tbh. But thats not important here.

            Here is a demo:

            ...

            ANSWER

            Answered 2020-May-15 at 12:48

            Using jQuery you can use $(mutation.target).index().

            Source https://stackoverflow.com/questions/61796787

            QUESTION

            Hierarchical array to set for use with jsTree
            Asked 2020-Mar-19 at 20:12

            I'm trying to create function that convert hierarchical data stored in array with following format: id, name, idType, members, idParent to text, children.

            The data of array:

            ...

            ANSWER

            Answered 2020-Mar-19 at 20:12

            QUESTION

            How to merge dataframes ? Error in UseMethod("tbl_vars") : no applicable method for 'tbl_vars' applied to an object of class "list"
            Asked 2020-Mar-06 at 12:57

            I am trying to merge two dataframes, one containing variables like Date, Author, Paper, and IDs, the other containing texts and their IDs. I add, because it might have some importance, that the dataframe containing the texts has been obtained by converting a Vcorpus into a dataframe with the following code :

            ...

            ANSWER

            Answered 2020-Mar-06 at 12:57

            There seems to be a problem with your reading function.

            The output is not a common dataframe object, but rather some sort of list containing only a dataframe object.

            Indeed, this line seems to work and give a proper merged dataframe:

            Source https://stackoverflow.com/questions/60552264

            QUESTION

            Intelij extract method keeps trying to replace duplicate method signatures - please stop
            Asked 2020-Feb-17 at 15:56

            Intellij has a really neat feature, that lets me seamlessly extract a block of code into its own method. I can then give this method a nice, descriptive name and move on with life.

            However, intellij also tries to find other blocks of code that are similar, and then tries to perusade me that I should also refactor them too, to use this new method its made. And then, when I hit the oddly-named "cancel" button (which implies the whole operation is cancelled, but it's not, it just stops asking about any remaining blocks), it leaves me looking at whatever the block of code it last asked me about.

            I really don't like this feature. Here's why: If I'm say comparing two ints - the naming of the code block will depend on the context of those two ints, but intellij will find any comparison between two ints anywhere in that file, and then insist that this is also a candidate for extraction.

            Most times it is not, and to make it worse, when I ask intellij to stop it, in a fit of pique, leaves me wherever the last comparison was, so now I have to navigate back to where I was working.

            How do I tell intellij just to extract exactly what I selected, and do nothing else?

            ...

            ANSWER

            Answered 2020-Feb-17 at 15:56

            Please follow/vote/comment the issue created for this usability problem at YouTrack: https://youtrack.jetbrains.com/issue/IDEA-233201

            Source https://stackoverflow.com/questions/60192576

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

            Vulnerabilities

            No vulnerabilities reported

            Install pique

            You can install using 'pip install pique' or download it from GitLab, GitHub, PyPI.
            You can use pique like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

            Support

            Pique was written by Russell Neches, a graduate student in Jonathan Eisen's laboratory.
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            Install
          • PyPI

            pip install pique

          • CLONE
          • HTTPS

            https://github.com/ryneches/pique.git

          • CLI

            gh repo clone ryneches/pique

          • sshUrl

            git@github.com:ryneches/pique.git

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