epic | diffuse domain ChIP-Seq caller | Genomics library

 by   biocore-ntnu Python Version: Current License: MIT

kandi X-RAY | epic Summary

kandi X-RAY | epic Summary

epic is a Python library typically used in Artificial Intelligence, Genomics applications. epic has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has high support. You can download it from GitHub.

epic is a software package for finding medium to diffusely enriched domains in chip-seq data. It is a fast, parallel and memory-efficient implementation of the incredibly popular SICER algorithm. By running epic on a set of data ("ChIP") files and control ("Input") files, epic is able to quickly differentially enriched regions. epic is an improvement over the original SICER by being faster, more memory efficient, multicore, and significantly much easier to install and use. The MIT-licensed code is available at The documentation is currently being worked on.
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            kandi-support Support

              epic has a highly active ecosystem.
              It has 32 star(s) with 7 fork(s). There are 5 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 27 open issues and 59 have been closed. On average issues are closed in 127 days. There are no pull requests.
              OutlinedDot
              It has a negative sentiment in the developer community.
              The latest version of epic is current.

            kandi-Quality Quality

              epic has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              epic is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              epic releases are not available. You will need to build from source code and install.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.
              epic saves you 1519 person hours of effort in developing the same functionality from scratch.
              It has 3385 lines of code, 176 functions and 71 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed epic and discovered the below as its top functions. This is intended to give you an instant insight into epic implemented functionality, and help decide if they suit your requirements.
            • Create a pandas dataframe for a given chromosome
            • Remove bins that are out of bounds out of a given chromosome
            • Get a dataframe for a chromosome
            • Count reads in the given bed file
            • Determine the options for the given bed file
            • Removes outliers from a dataframe
            • Convert island counts to pvalue
            • Logical factorial
            • Poisson function for Poisson distribution
            • Create a cluster bigwig
            • Create a biwig
            • Convert list to integers
            • Merge chromosome and input data
            • Add color breaks to the dataframe
            • Reads a genome size file
            • Get genome size file
            Get all kandi verified functions for this library.

            epic Key Features

            No Key Features are available at this moment for epic.

            epic Examples and Code Snippets

            No Code Snippets are available at this moment for epic.

            Community Discussions

            QUESTION

            Javascript DIV scroll to bottom by class name not working
            Asked 2021-Jun-15 at 17:24

            I have a div which with long content and that is why the scrollbar is coming. I want when user click on a button. Then, the div scroll bar goes to end of the content. I tried this way but no luck.

            I want to achieve this without using jQuery.

            ...

            ANSWER

            Answered 2021-Jun-15 at 15:58

            You don't actually need javascript. A simple link will do. You can also do it with javascript, but I see no reason to in this case.

            This would work:

            Source https://stackoverflow.com/questions/67989561

            QUESTION

            React - setTimeout inside promise flashes UI elements, randomly returns array undefined
            Asked 2021-Jun-12 at 08:01

            I'm trying to make a tic-toc game without using classes and with player-computer. The whole code in codesandbox.io

            The piece of code, where the problems appear:

            ...

            ANSWER

            Answered 2021-Jun-12 at 08:01

            There are few things that need to be fixed.

            1. In your handleClick, you are using setSquares((squares) => squares.splice(i, 1, "X")). squares.splice will mutate the state variable squares which one should never do.
            2. Also splice doesn't return updated array but

            An array containing the deleted elements.

            This causes squares from [null, null, null, null, null, null, null, null, null] to [null] causing you board to become blank for a moment. Then your setSquares((squares) => [...squares2]) kicks in from setTimeout making squares back to array making your square values visible again hence, the flash.

            1. computersTurnHandler might return undefined in some cases where none of the return statements trigger hence

            Uncaught TypeError: squares2 is undefined handleClick Board.js:34

            1. You need to prevent user from clicking until your setTimeout is complete else multiple rapid clicks by user will cause inconsistent behaviour.

            As for your query

            is it acceptable at all to use Promises in that case

            Usually situations like these can simply be solved by making use of temporary variable in most cases.

            Now the Solution with promise and fixed handleClick and computersTurnHandler is as follows

            Source https://stackoverflow.com/questions/66943500

            QUESTION

            Change Azure DevOps Parent Work Item status when all linked children work items meet certain condition?
            Asked 2021-Jun-04 at 02:57

            I see there are plenty of options for creating custom rules in Azure DevOps, but I don't see one (or perhaps I'm not interpreting it correctly), that handles this scenario.

            I have an Epic. That Epic has a state of "In Progress".

            That Epic has 10 user stories as linked child items. Each Story has a state as well.

            Can I create a rule that when all 10 of those stories stages reach "Done", then the parent Epic will automatically change state to "Done"?

            Any thoughts on how to do this?

            ...

            ANSWER

            Answered 2021-Jun-04 at 02:57

            As of this time, however, automate state transitions of parent work items by Azure DevOps process rules is not supported.

            But you can add a web hook and use the code and configuration provided in the Automate State Transitions GitHub project.

            Click this link for detailed information about setting up the project.

            Source https://stackoverflow.com/questions/67827937

            QUESTION

            Default SimpleTransformers setup fails with ValueError str
            Asked 2021-May-31 at 21:12

            I'm trying to use SimpleTransformers default setup to do multi-task learning.

            I am using the example from their website here

            The code looks like below:

            ...

            ANSWER

            Answered 2021-May-30 at 17:54

            In the example code if you change

            Source https://stackoverflow.com/questions/67755780

            QUESTION

            Invalid argument(s) (input): Must not be null - Flutter
            Asked 2021-May-30 at 11:07

            Am building a movies App where i have list of posters loaded using TMDB using infinite_scroll_pagination 3.0.1+1 library. First set of data loads good but after scrolling and before loading second set of data i get the following Exception.

            ...

            ANSWER

            Answered 2021-May-30 at 10:18

            In Result object with ID 385687 you have a property backdrop_path being null. Adjust your Result object and make the property nullable:

            String? backdropPath;

            Source https://stackoverflow.com/questions/67755803

            QUESTION

            The type returned by `createAction` isn't maintained through `ofType`
            Asked 2021-May-30 at 03:41

            I'm making an app that lets the user select snacks from a list of available snacks. The snacks are loaded from an external API.

            I'm using redux-observable to "listen" for actions and then dispatch the appropriate API requests. Here's my existing code, with a comment on the problematic line of code:

            ...

            ANSWER

            Answered 2021-May-30 at 03:33

            If I use filter and .match then the correct type is inferred:

            Source https://stackoverflow.com/questions/67755504

            QUESTION

            How can I loop over an array of arrays created with flat()?
            Asked 2021-May-24 at 11:39

            I have combined 3 JSON files into a single array using flat(), and then looped through the array to output its contents in the console. It outputs an array of arrays created from the 3 JSON files below.

            Here's the console output:

            ...

            ANSWER

            Answered 2021-May-24 at 11:39

            I'm not sure if this is exactly what you wanted, cause you didn't specify exact output, but I think you get a point how can it be done.

            Object.entries / Object.keys / Object.values is something what you are looking for:

            Source https://stackoverflow.com/questions/67664655

            QUESTION

            Python request() to get json giving different body in browser than in script
            Asked 2021-May-22 at 19:07

            I'm trying to get a json from this URL doing a request with python. Problem is that I'm getting a different body if I use a browser than if I use a python request. The URL is the follwing:

            https://api.tracker.gg/api/v2/rocket-league/standard/profile/epic/nosumable

            The body contains the json I want to download.

            This is the code I'm using to get the json:

            ...

            ANSWER

            Answered 2021-May-22 at 19:07

            Add a user agent to your GET requests.

            Source https://stackoverflow.com/questions/67653178

            QUESTION

            What components are required to setup batch data ingestion from EPIC EMR to Azure FHIR API (Paas)?
            Asked 2021-May-21 at 13:37

            I'm trying to create a demo to connect a new Azure FHIR api which I created with EPIC(EMR) to ingest the data in batch mode, I'm unable to find out what all components/pieces are required to setup that ingestion pipeline. The examples that are shown in the available videos are related to pumping the data manually. I want to achieve something like Web-Jobs approach. I don't need the exact code or very detailed solution. It's just if I can have the lists of components and in what way they will be connected to make this ingestion pipeline work.

            ...

            ANSWER

            Answered 2021-May-21 at 13:37

            If you are looking for Epic-specific support, I'd recommend reaching out to open@epic.com, (Epic's free, public support option), joining App Orchard (Epic's paid support option), or working with the healthcare organization's IT team directly.

            That said, if you are looking at extracting data from Epic, and loading it into the Azure data warehouse (I'm reading between the lines and guessing your use case), we've heard of several folks looking to do that. Right now, there is not a good FHIR-based method of doing data warehouse synchronization that is supported by Epic. There are good non-FHIR options though (SQL extracts or HL7v2 event driven messaging). If you are using the Azure FHIR storage option, you'll need to do a data transform, but that is a far better option than trying to use an inferior exchange paradigm.

            Source https://stackoverflow.com/questions/67627197

            QUESTION

            Vuetify Tabs with Router and dynamic nested routes
            Asked 2021-May-21 at 05:16

            I'm pretty new to Vue. My app has a pretty standard layout with top nav, side nav, footer and a content area. Content area is divided into two with a tree on the left and a Tabbed interface on the right. I'm using vue router with nested dynamic routes.

            TreeAndTab.vue

            ...

            ANSWER

            Answered 2021-May-21 at 05:16

            Finally I was able to fix it.Looks like route on the tabs were not setup correctly. Here's what I changed:

            1. Moved tabProps to compute() to update route on the fly.
            2. Fired an event from child component to update the route which gets caught by the parent that updates the route.
            3. I did not use this.$route to update the tab route dynamically since I wanted to retain the state of the second tab if a child node is selected on the tree but the user switches to the first tab which contains data for the parent. (I know its confusing). So its like a file explorer where first tab shows details of the folder and second tab shows details of the selected child in that folder.

            Tab states are now maintained.

            Here's the relevant code (not the most efficient but it works). Hopefully, it helps someone facing similar issue.

            route.js

            Source https://stackoverflow.com/questions/67597969

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

            Vulnerabilities

            No vulnerabilities reported

            Install epic

            epic is available for python2.7 and above. It can be installed from the Python Package Index with pip install bioepic or preferably from bioconda with conda install -c bioconda epic, or by cloning the repo at https://github.com/endrebak/epic and running python setup.py install.

            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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            CLONE
          • HTTPS

            https://github.com/biocore-ntnu/epic.git

          • CLI

            gh repo clone biocore-ntnu/epic

          • sshUrl

            git@github.com:biocore-ntnu/epic.git

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