driveR | Prioritizing Cancer Driver Genes Using Genomics Data | Genomics library

 by   egeulgen R Version: v0.3.0 License: Non-SPDX

kandi X-RAY | driveR Summary

kandi X-RAY | driveR Summary

driveR is a R library typically used in Artificial Intelligence, Genomics applications. driveR has no bugs, it has no vulnerabilities and it has low support. However driveR has a Non-SPDX License. You can download it from GitHub.

Cancer genomes contain large numbers of somatic alterations but few genes drive tumor development. Identifying cancer driver genes is critical for precision oncology. Most of current approaches either identify driver genes based on mutational recurrence or using estimated scores predicting the functional consequences of mutations. driveR is a tool for personalized or batch analysis of genomics data for driver gene prioritization by combining genomics information and prior biological knowledge. As features, driveR uses coding impact metaprediction scores, non-coding impact scores, somatic copy number alteration scores, hotspot gene/double-hit gene condition, ‘phenolyzer’ gene scores and memberships to cancer-related KEGG pathways. It uses these features to estimate cancer-type-specific probabilities for each gene of being a cancer driver using the related task of a multi-task learning classification model. The method is described in detail in Ülgen E, Sezerman OU. driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. BMC Bioinformatics. 2021 May 24;22(1):263.
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            kandi-support Support

              driveR has a low active ecosystem.
              It has 9 star(s) with 0 fork(s). There are 1 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 2 open issues and 2 have been closed. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of driveR is v0.3.0

            kandi-Quality Quality

              driveR has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              driveR has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              driveR releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

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            driveR Key Features

            No Key Features are available at this moment for driveR.

            driveR Examples and Code Snippets

            ,Installation
            Rdot img1Lines of Code : 3dot img1License : Non-SPDX (NOASSERTION)
            copy iconCopy
            install.packages("driveR")
            
            # install.packages("devtools")
            devtools::install_github("egeulgen/driveR", build_vignettes = TRUE)
              

            Community Discussions

            QUESTION

            How to deal with spaces in a HTML/JavaScript class name
            Asked 2021-Jun-15 at 20:06

            I am having problems getting data from a element using Selenium with the line:

            ...

            ANSWER

            Answered 2021-Jun-15 at 20:06

            When an element has spaces in the class attribute, that means it has multiple classes, so you'll need to handle that another way.

            One option is with CSS selectors.

            https://selenium-python.readthedocs.io/locating-elements.html#locating-elements

            https://selenium-python.readthedocs.io/api.html#locate-elements-by

            Source https://stackoverflow.com/questions/67992425

            QUESTION

            Unable to make a migration. Getting errors related to foreign keys
            Asked 2021-Jun-15 at 18:27

            First migration file:

            ...

            ANSWER

            Answered 2021-Jun-15 at 18:27

            change the posts migration post_id and author_id to this :

            Source https://stackoverflow.com/questions/67976654

            QUESTION

            VBA - NULL values in Listview
            Asked 2021-Jun-15 at 17:10

            I've created a simple VBA interface to connect Excel to a MySQL DB. The VBA part acts as a preview of data for the user to choose what item he wants to import to the Excel sheet.

            Until now I've work with a very complete set of data, but I got to a Table which (because of the nature of the items) some fields are NULL.

            Now every time I try to check the values in the VBA I get the Run-time error 13 Type mismatch in the listview component. At first I though it was a field with DECIMAL typing, but after changing it to a DOUBLE (for testing) the problem persisted, and it was until I notice that if only checks columns with no NULL value, the problem disappears. Off course I can't omit this values.

            I tried some .Tostring functions but with no success. And I failed to implement a IF to check for NULL in the obj.

            This is my code:

            ...

            ANSWER

            Answered 2021-Apr-13 at 10:28

            If you don't want to add a IsNull-function in you SQL (as Nathan_Sav suggested as a comment): There is a IsNull-function in VBA. With that, you can create a simple function that returns for example an empty string (or a 0 or whatever you prefer):

            Source https://stackoverflow.com/questions/67072643

            QUESTION

            How to run Sequelize migrations inside Docker
            Asked 2021-Jun-15 at 15:38

            I'm trying to docerize my NodeJS API together with a MySQL image. Before the initial run, I want to run Sequelize migrations and seeds to have the tables up and ready to be served.

            Here's my docker-compose.yaml:

            ...

            ANSWER

            Answered 2021-Jun-15 at 15:38

            I solved my issue by using Docker Compose Wait. Essentially, it adds a wait loop that samples the DB container, and only when it's up, runs migrations and seeds the DB.

            My next problem was: those seeds ran every time the container was run - I solved that by instead running a script that runs the seeds, and touchs a semaphore file. If the file exists already, it skips the seeds.

            Source https://stackoverflow.com/questions/67765749

            QUESTION

            I am using a IF condition to select the element getting error as no such element
            Asked 2021-Jun-15 at 15:03

            In the below code i am getting error as no such element but when i try with out if condition its working fine

            String currenturl= driver.getCurrentUrl(); String UK="gben",NZ="nzen",SE="sesv",AU="auen",NL="nlnl",NO="nonb",IE="ieen",DK="dkda",FI="fifi"; if (currenturl.contains("NL||NO||IE||DK||FI||SE")) { driver.findElement(By.cssSelector("#ss-nav-primary__item--menu-bbb-glasses > a")).click(); } else if(currenturl.contains("NZ||UK")) { driver.findElement(By.cssSelector("#ss-nav-primary__item--menu-glasses > a")).click(); } else { driver.findElement(By.cssSelector("#ss-nav-primary__item--menu-new-test > a")).click(); }

            ...

            ANSWER

            Answered 2021-Jun-15 at 15:03

            Your condition is wrong.
            Instead of

            Source https://stackoverflow.com/questions/67987392

            QUESTION

            Selenium Element not intractable
            Asked 2021-Jun-15 at 15:02

            Weird case happening here. I am trying to insert some keys in a username and password input field. It was working just fine and suddenly it did stop.

            Just to make thing clear for everyone. Once I click on login button, I get redirected to the login page where I have my username and password input fields. and their divs are as follow.

            in my selenium code I target the username and password element by their name.

            ...

            ANSWER

            Answered 2021-Jun-15 at 15:02

            I think you need ExplicitWait :

            try this :

            Source https://stackoverflow.com/questions/67987992

            QUESTION

            My JCheckBox program only displays one box. Why is that?
            Asked 2021-Jun-15 at 14:34

            I am attempting to add another checkbox to this program but for some reason it will not display when I run the program. Only the check box for the blue pill displays. I have attempted to add a couple things or change the way the program is structured, but nothing I have done so far has helped.

            Code Below:

            ...

            ANSWER

            Answered 2021-Jun-15 at 04:38

            When you're stuck on a problem, it never hurts to go back and consult the documentation.

            You'll find information like this:

            A border layout lays out a container, arranging and resizing its components to fit in five regions: north, south, east, west, and center. Each region may contain no more than one component, and is identified by a corresponding constant: NORTH, SOUTH, EAST, WEST, and CENTER. When adding a component to a container with a border layout, use one of these five constants...

            When you add your button, you do this:

            Source https://stackoverflow.com/questions/67979964

            QUESTION

            Can different network be the cause for UnreachableBrowserException exception?
            Asked 2021-Jun-15 at 13:57

            I have two grid setup's

            1. Local grid setup (hub and nodes are running in my local machine) and my local machine connected to network#1

            2. VM grid setup (hub and nodes are running in my virtual machine) and my virtual machine connected to network#2

            When I execute the scripts I need to pass the IP address as a parameter. Here, I can run my scripts successfully in local machine(code is available in local machine) by passing the network#1 IP address but if I pass the network#2 IP address (VM IP address) to local machine then I am getting below exception,

            org.openqa.selenium.remote.UnreachableBrowserException: Could not start a new session. Possible causes are invalid address of the remote server or browser start-up failure.

            As per my knowledge, hub and nodes should be connected to same network. Cannot we run the scripts by passing the VM IP address to local machine?

            Trace:

            ...

            ANSWER

            Answered 2021-Jun-15 at 13:57

            Yes, the exception occurred due to firewall. The ping test is successful from local machine to VM but not from VM to local. I contacted the organization network administrator to confirmed this.

            Source https://stackoverflow.com/questions/67836113

            QUESTION

            Method Illuminate\\Auth\\RequestGuard::attempt does not exist
            Asked 2021-Jun-15 at 13:13

            I just install Laravel passport as follow:

            Admin Model:

            ...

            ANSWER

            Answered 2021-Jun-15 at 13:13

            The issue with default guard. So it should be web

            Source https://stackoverflow.com/questions/67986476

            QUESTION

            Selenium Testing unable to target element
            Asked 2021-Jun-15 at 13:10

            I am running some testing on our website using selenium. At the login page I would like to target the login button and click it.

            the source code of the page looks like this:

            I am trying to target the second button that has the class=OTSigninButton by using its xpath.

            so here is the python code.

            ...

            ANSWER

            Answered 2021-Jun-15 at 13:10

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

            Vulnerabilities

            No vulnerabilities reported

            Install driveR

            You can install the latest released version of driveR from CRAN via:.

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            gh repo clone egeulgen/driveR

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