idep | Integrated Differential Expression and Pathway analysis | Genomics library

 by   iDEP-SDSU R Version: Current License: No License

kandi X-RAY | idep Summary

kandi X-RAY | idep Summary

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

Integrated Differential Expression and Pathway analysis
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            kandi-support Support

              idep has a low active ecosystem.
              It has 116 star(s) with 57 fork(s). There are 14 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 82 open issues and 65 have been closed. On average issues are closed in 1270 days. There are 3 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of idep is current.

            kandi-Quality Quality

              idep has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              idep 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

              idep releases are not available. You will need to build from source code and install.
              Installation instructions, examples and code snippets are available.

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            idep Key Features

            No Key Features are available at this moment for idep.

            idep Examples and Code Snippets

            No Code Snippets are available at this moment for idep.

            Community Discussions

            QUESTION

            Issue: C compiler used for C++ in CMake | CMake + git
            Asked 2021-May-28 at 13:28

            I've been using CMake to build my next C++ project, and I had to link a library named 'GLFW' to my executable. I've been having strange issues with this:

            Here is my project structure

            GLFW is cloned into the 'dep' directory. The 'build' directory is my CMake build directory. The 'src' directory is a subdirectory to my top-level CMakeLists.txt and contains the source code.

            Top-level CMakeLists.txt:

            ...

            ANSWER

            Answered 2021-May-28 at 13:28

            Your project is fine. You just happened to run into a bug within glfw: https://github.com/glfw/glfw/issues/1807

            It's been fixed already, but not released yet. So your best options are to clone the master branch, or to manually apply whichever fix resolved the issue in your version of the source until 3.3.5 gets released.

            Source https://stackoverflow.com/questions/67728467

            QUESTION

            D3 v4 change opacity for kontext related nodes
            Asked 2020-Dec-10 at 15:58

            I am completely new to D3 and trying to solve the following scenario. I got several context related nodes in place. All of them are displayed fine as I want to, further I want to add an HTML selector button which changes the colour and opacity of all nodes, which are not selected.

            The Goal is to highlight the selection by changing the non selected nodes colour and opacity. I do not want completely remove them as done here because some nodes are will be member of more than one context in future.

            I thought the swarm intelligence of our community might got an idea. Thanks in advance.

            ...

            ANSWER

            Answered 2020-Dec-10 at 15:57

            You'll want the select menu to have values representing each kontext:

            Source https://stackoverflow.com/questions/65229802

            QUESTION

            DryIoc ScopedTo now includes parent scope?
            Asked 2020-Jul-14 at 13:30

            The code below worked in DryIoc 2.x. I just updated to 4.x. The code no longer works (see the exception below). It appears that 4.x treats the "ScopedTo" data as non-exclusive, whereas in 2.x they were exclusive to the scope -- they weren't available to other scopes out of the box. How do I get the 2.x behavior now? The exception lists several remedies, but which remedy matches the 2.x behavior?

            ...

            ANSWER

            Answered 2020-Jul-14 at 13:30

            Seems like a bug. I have created the respective issue in DryIoc repository https://github.com/dadhi/DryIoc/issues/290. Please move the discussion there.

            The issue will appear only with Reuse.Singleton parent services. So until the issue is fixed, the workaround may be to change Owner reuse or to insert artificial scope to play the role of a singleton for those services.

            Update

            DryIoc v4.2.4 with the fix is out on NuGet https://github.com/dadhi/DryIoc/releases/tag/v4.2.4

            Source https://stackoverflow.com/questions/62883828

            QUESTION

            PocketSphinx install can't find swig.exe
            Asked 2020-May-16 at 10:27

            I have searched all over the web and especially have gone through all the questions regarding this here on Stackoverflow.

            I am using the following command to install it "pip install pocketsphinx"

            I have windows x64, I have not set any environmental paths regarding Swig.

            Also I've downloaded Swig zip file and extracted it into my downloads folder, searched through it and there is no "swig.exe" file.

            Below you can see the error/log from the command prompt.

            ...

            ANSWER

            Answered 2018-Jan-14 at 12:08

            Alright, I solved it. Here’s how:

            First I went to their official website and downloaded the swigwin file specifically for windows with a “swig.exe” file.

            Then I extracted it, and added it to the environment variable PATH. This solved my problem.

            Afterwards I got another error, it couldn’t find visual studio C++ build tools v14.0 (along these lines), if you have this problem too just, download the C++ build tools 2015 from their official website, install, then find it in your Program Files or what ever, copy the path to the VC folder and add it to your environment variable PATH as well.

            This allowed me to download/install pocketsphinx on windows.

            Source https://stackoverflow.com/questions/48232527

            QUESTION

            library pocketsphinx not downloading using pip or binary files
            Asked 2020-Apr-30 at 16:01

            I am working on a speech recognition software and wanted to test out pocketsphinx and have tried to install it using pip on windows 10 python version 3.8 and it wont download usually i would fix the problem by downloading it as binary file and then trying to install it but it tells me that the whl file is unsupported and thank you all in advance.

            Down below is the error message I got.

            ...

            ANSWER

            Answered 2019-Oct-30 at 15:42

            ERROR: pocketsphinx-0.1.15-cp36-cp36m-win32.whl is not a supported wheel on this platform

            You're trying to install a wheel for Python 3.6 to Python 3.8. That doesn't work.

            The latest release of pocketsphinx was released at Jun 4, 2018, more than a year ago. Python 3.8 didn't exist at that time so they don't provide wheels for it.

            Actually they don't even have wheels for Python 3.7. Either you have to use Python 3.6 or compile the project from sources. To compile from sources you need a number of prerequisites.

            The error

            error: command 'swig.exe' failed: No such file or directory

            means that you miss one of the prerequisites — SWIG.

            Source https://stackoverflow.com/questions/58628522

            QUESTION

            Makefile on C++ SDL2
            Asked 2020-Mar-04 at 11:21

            I'm using C++ SDL2 and trying to load 3 .cpp files as well as 2 .h files.

            I got this error message:

            ...

            ANSWER

            Answered 2020-Mar-04 at 11:21

            Solved! -lmingw32 had to be removed, answers the multiple definition of `main' error as well

            EDIT: using VS 2019 command prompt

            Source https://stackoverflow.com/questions/60515496

            QUESTION

            Installing pocketsphinx python module: command 'swig.exe' failed
            Asked 2020-Mar-03 at 08:59

            I'm getting something like this. Can anyone please tell me how to fix this.

            ...

            ANSWER

            Answered 2017-Jun-12 at 19:23

            You try to install pocketsphinx with pip, that will download and compile this module. It requires some compiling tool like swig.

            Another solution is to install a binary version of pocketsphinx. You can download a binary version here. You have to select the correct version with respect to your installation.

            To determine which one you have to download, you can run the following commands, that will tell you which version you require and whether you run a 32 or 64 bit python interpreter.

            Source https://stackoverflow.com/questions/44504899

            QUESTION

            bootsrap changes dropdown menu code to something too complicated
            Asked 2019-Oct-24 at 11:05

            I am using this theme material design https://gurayyarar.github.io/AdminBSBMaterialDesign/ to create a codeigniter application and I have a problem with the dropdown because it changes the code from this :

            ...

            ANSWER

            Answered 2019-Oct-24 at 11:05

            It is because theme material design includes custom select code for that. If you don't want it then remove custom select code. For custom select code like this or it's targeted on class(form-control show-tic).

            Source https://stackoverflow.com/questions/58538883

            QUESTION

            Couldn't install textract in google colab
            Asked 2019-Jun-27 at 09:13

            I couldn't install textract in google colab, error message showing as below.

            some people suggest to use sudo apt-get install libasound2-dev but how to do sudo... in google colab?

            === error message ==========================================================

            Failed building wheel for pocketsphinx Running setup.py clean for pocketsphinx Failed to build pocketsphinx Installing collected packages: pocketsphinx Running setup.py install for pocketsphinx ... error Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-install-03c_ysbm/pocketsphinx/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-record-6n9ewg9i/install-record.txt --single-version-externally-managed --compile: running install running build_ext building 'sphinxbase._sphinxbase' extension swigging deps/sphinxbase/swig/sphinxbase.i to deps/sphinxbase/swig/sphinxbase_wrap.c swig -python -modern -threads -Ideps/sphinxbase/include -Ideps/sphinxbase/include/sphinxbase -Ideps/sphinxbase/include/android -Ideps/sphinxbase/swig -outdir sphinxbase -o deps/sphinxbase/swig/sphinxbase_wrap.c deps/sphinxbase/swig/sphinxbase.i unable to execute 'swig': No such file or directory error: command 'swig' failed with exit status 1

            =========================================================================== Thank you, Ling

            ...

            ANSWER

            Answered 2019-Jan-10 at 06:26

            In google colab Bash commands run by prefixing the command with ‘!’.

            Example:

            Source https://stackoverflow.com/questions/54122807

            QUESTION

            'wchar.h' file not found
            Asked 2019-Apr-14 at 09:51

            I know about this question: macOS 'wchar.h' File Not Found but it did not help me. I've tried reinstalling xcode, reinstalling command line tools, restarting the system. wchar.h file is in place, but the compiler does not manage to find it. What else could I try? Maybe it is sysroot related? Any way to fix that?

            ...

            ANSWER

            Answered 2017-Sep-21 at 16:41

            It was caused by incorrect sysroot, (set for an older mac os version) set in makefiles.

            Source https://stackoverflow.com/questions/46342411

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

            Vulnerabilities

            No vulnerabilities reported

            Install idep

            Local installation of this software is possible through steps below. But it is not supported or updated freqently. Local install is for non-profit organizations only. For-profit businesses please contact us. iDEP and ShinyGO are both under active development, thanks to a grant from NHGRI. They have not been fully tested. So we are constantly fixing bugs/errors in both source code and sometime database. If you install locally, please make sure to check for updates regularily here and download the latest versions of both the source code and database. For most users, we recommend to visit our website.
            Cloud computing providers such as Amazon AWS provides temporary servers that can be used inexpensively, especially the spot instances. See this video for some step-by-step screen-shot. The setup.sh script was tested only on Ubuntu. Wait until the script shows 'iDEP docker images and databases are ready!'. Now the server is running with 10 containers to serve many concurrent users. You should be able to use iDEP from a web browser with http://12.12.12.12/idep94/, where 12.12.12.12 is the IP address of the server. ShinyGO can used via http://12.12.12.12/go74/. The server's port 80 should be available and exposed. A user has contributed scripts to install a standalone version using Singularity. Following the instruction in this folder.
            More than 250GB available storage
            More than 4GB memory
            A Linux system with port 80 open for web access.
            Install Git, if it is not available. For Ubuntu:
            Install Docker
            Install Docker-compose
            Copy iDEP source code from GitHub. Here we are installing iDEP in the home directory; change to other folder if desired.
            Download docker images from DockHub, and download database file from our FTP server. It can take as much as 2 hours, as the script downloads and unzips large files. Once finished total storage usage is about 161GB!
            Start the Shiny server with Docker-compose from the idep folder.

            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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          • HTTPS

            https://github.com/iDEP-SDSU/idep.git

          • CLI

            gh repo clone iDEP-SDSU/idep

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            git@github.com:iDEP-SDSU/idep.git

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