dREG | Detecting Regulatory Elements using GRO-seq and PRO-seq | Genomics library

 by   Danko-Lab R Version: Current License: No License

kandi X-RAY | dREG Summary

kandi X-RAY | dREG Summary

dREG is a R library typically used in Artificial Intelligence, Genomics, Neural Network applications. dREG has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Detecting Regulatory Elements using GRO-seq and PRO-seq
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            kandi-support Support

              dREG has a low active ecosystem.
              It has 29 star(s) with 18 fork(s). There are 11 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 6 open issues and 2 have been closed. On average issues are closed in 26 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of dREG is current.

            kandi-Quality Quality

              dREG has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              dREG 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

              dREG releases are not available. You will need to build from source code and install.
              Installation instructions are not available. Examples and code snippets are available.
              It has 70 lines of code, 0 functions and 2 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

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            dREG Key Features

            No Key Features are available at this moment for dREG.

            dREG Examples and Code Snippets

            No Code Snippets are available at this moment for dREG.

            Community Discussions

            QUESTION

            Merge items in an array including sub items
            Asked 2021-Dec-19 at 09:35

            I have an array that is as follows:

            ...

            ANSWER

            Answered 2021-Dec-19 at 09:16

            You cannot have an object with two identical keys like

            Source https://stackoverflow.com/questions/70409970

            QUESTION

            AVR External Interrupts Triggering in Assembly
            Asked 2021-Nov-27 at 21:23

            I would like to change Arduino Nano (ATMega328p) led pin (13 - PB5) state by triggering an External Interrupt (using pin INT0 - PD2) in AVR Assembly Code.

            I am using Atmel's avrasm2 assembler to compile to .hex file. The code is:

            ...

            ANSWER

            Answered 2021-Nov-27 at 21:23

            You used wrong instruction to save value to EIMSK. EIMSK isn't memory mapped. You should use out instruction

            Source https://stackoverflow.com/questions/69876796

            QUESTION

            How to centre side by side radio buttons on page
            Asked 2021-Aug-02 at 06:07

            I've created side-by-side radio buttons and have tried to center them on my web page but one of the buttons doesn't move when I'm editing the margin sizes. I would like to move the left button more to the left.

            My HTML code:

            ...

            ANSWER

            Answered 2021-Aug-02 at 00:30

            Try this code. If this is not what you want, let me know.

            Source https://stackoverflow.com/questions/68615293

            QUESTION

            Yacc prints a different union variable than the one specified
            Asked 2021-May-15 at 08:30

            I am trying to implement a calculator in flex/yacc that will also support real numbers ( i have not implemented them yet). But for some reason instead of printing the value of the expression my code only prints the type of the expression which is 1 for integers. Here's the flex file

            ...

            ANSWER

            Answered 2021-May-15 at 08:30

            Each token and grammar rule can use only one value from the union and not the whole union as a struct.

            Source https://stackoverflow.com/questions/67516215

            QUESTION

            performing Groupby in large data set MySQL
            Asked 2021-Jan-07 at 22:27

            I have data like this in my table in success column 1 -> success 0 -> failed

            ...

            ANSWER

            Answered 2021-Jan-06 at 08:52

            Using conditional aggregation with boolean expressions we can try:

            Source https://stackoverflow.com/questions/65592713

            QUESTION

            How to catch GenServer.call(destination, ...) failure when destination process doesn't exist
            Asked 2020-Sep-06 at 06:40

            In my application all logged users are represented by a GenServer, I call a UserAgent, which basically keeps in memory the state of each user. All those processes are registered across the cluster in a distributed registry based on Horde with a unique ID. Whenever the user does some action, the client application sends the action to be performed along with the user_id. On server side, the controller checks the parameters (mandatory, optional, syntax, etc) and eventually calls UserAgent.the_action(user_id, other_params). The the_action(...) function simply sends a message to the server with the action to be performed: GenServer.call(via_tuple(id), {:the_action, params}).

            In some cases, the UserAgent referenced by user_id doesn't exist any more, for example because the user had been inactive for some time and the process had been cleaned out (the sesion had expired) or because parts of the cluster are not reachable at that moment (imaginary use case for the moment). In those situations the call GenServer.call(via_tuple(id), {:the_action, params}) results in the error below which also crashes the HTTP endpoint process (#PID<0.1359.0> below) which in turn results in a 500 HTTP error (the dump api call, well, dumps the state of a process for debug purposes):

            ...

            ANSWER

            Answered 2020-Sep-06 at 06:40

            This is how GenServer.call/3 handles errors in elixir. It nevertheless calls whereis/1, so you might either call whereis/1 yourself or replicate logic from the code I linked or use Kernel.SpecialForms.try/1 to catch the exception.

            Source https://stackoverflow.com/questions/63761341

            QUESTION

            Kubernetes overlay mounts and rsync
            Asked 2020-Jul-29 at 23:41

            I'm trying to tweak my Kubernetes-based app to make it more development-friendly. I'm using kustomize to add some extra containers into my app-deployment. It looks like this:

            ...

            ANSWER

            Answered 2020-Jul-29 at 23:41

            No, Kuberentes mounts, unlike Docker mounts do not allow mounting one directory over the other. Potential VOLUME lines from the Dockerfile do not matter.

            A common solution for your use-case is, to use an init container to set up the emptyDir, before the main container is started. So basically you specify the emptyDir as a volume mount in both the init container and the main container and have the init container copy the files into the emptyDir.

            Additionally, there are two projects that offer different solutions to what you are trying to achieve:

            Using one of those you would not need the custom rsync and init container setup in your overlay.

            Source https://stackoverflow.com/questions/63096610

            QUESTION

            How to parse XML data into SQL query viewer
            Asked 2020-Jul-29 at 17:37

            I have a XML column in a SQL Server database that I need to be able to extract the data from, and spread into multiple columns in a SQL query. The table itself runs to multiple millions of rows of data.

            The XML data is stored as:

            ...

            ANSWER

            Answered 2020-Jul-29 at 17:37

            Try something like this to extract the separate XML elements under as separate values:

            Source https://stackoverflow.com/questions/63158416

            QUESTION

            `std::find()` producing weird results with strings
            Asked 2020-Apr-11 at 11:08

            I have a college assignment to write an Assembler for a given hypothetical instruction set. I have implemented it, and when I am debugging, the std::find() function I've implemented is giving weird results. Please help.

            ...

            ANSWER

            Answered 2020-Apr-11 at 11:08

            You are adding a null character to the tokens when you parse:

            Source https://stackoverflow.com/questions/61154652

            QUESTION

            Using envfit (vegan) to calculate species scores
            Asked 2020-Apr-09 at 23:15

            I am running an NMDS and have a few questions regarding the envfit() function in the vegan package. I have read the documentation for this function and numerous posts on SO and others about vegan, envfit(), and species scores in general.

            • I have seen both envfit() and wascore() used to calculate species scores for ordination techniques. By default, metaMDS() uses wascore(). This uses weighted averaging, which I understand. I am having a harder time understanding envfit(). Do envfit() and wascore( yield the same results? Is wascore() preferable given that it is the default? I realize that in some situations, wascore() might not be an option (ie. negative values), as mentioned in this post. How to get 'species score' for ordination with metaMDS()?

            • Given that envfit() and wascore() both seem to be used for species scores, they should yield similar results, right? I am hoping that we could do a proof of this here... The following shows species scores determined using metaMDS() using the default wascore():

            ...

            ANSWER

            Answered 2020-Apr-09 at 23:15
            Q: Do wascores() and envfit() give the same result?

            No they do not give the same result as these are doing two quite different things. In this answer I have explained how envfit() works. wascores() takes the coordinates of the points in the nmds space and computes the mean on each dimension, weighting observations by the abundance of the species at each point. Hence the species score returned by wascores() is a weighted centroid in the NMDS space for each species, where the weights are the abundances of the species. envfit() fits vectors that point in the direction of increasing abundance. This implies a plane over the NMDS ordination where abundance increase linearly from any point on the plane as you move parallel to the arrow, whereas wascores() are best thought of as optima, where the abundance declines as you move away from the weighted centroid, although I think this analogy is looser than say with a CA ordination.

            The issue about being optimal or not, is an issue if you passed in standardised data; as the answer you linked to shows, this would imply negative weights which doesn't work. Typically one doesn't standardise species abundances — there are transformations that we apply like converting to proportions, square root or log transformations, normalizing the data to the interval 0-1 — but these wouldn't give you negative abundances so you;re less likely to run into that issue.

            envfit() in an NMDS is not necessarily a good thing as we wouldn't expect abundances to vary linearly over the ordination space. The wascores() are better as they imply non-linear abundances, but they are a little hackish in NMDS. ordisurf() is a better option in general as it adds a GAM (smooth) surface instead of the plane implied by the vectors, but you can't show more than one or a few surfaces on the ordination, whereas you can add as many species WA scores or arrows as you want.

            The basic issue here is the assumption that envfit() and wascores() should give the same results. There is no reason to assume that as these are fundamentally different approaches to computing "species scores" for NMDS and each comes with it's own assumptions and advantages and disadvantages.

            Source https://stackoverflow.com/questions/60937869

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

            Vulnerabilities

            No vulnerabilities reported

            Install dREG

            You can download it from GitHub.

            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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            gh repo clone Danko-Lab/dREG

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