TMB | 肿瘤突变负荷学习笔记(tumor mutation burden) | Genomics library

 by   fanyucai1 Python Version: 1.0 License: No License

kandi X-RAY | TMB Summary

kandi X-RAY | TMB Summary

TMB is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. TMB has no bugs, it has no vulnerabilities and it has low support. However TMB build file is not available. You can download it from GitHub.

肿瘤突变负荷学习笔记(tumor mutation burden)
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            kandi-support Support

              TMB has a low active ecosystem.
              It has 8 star(s) with 10 fork(s). There are 3 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              TMB has no issues reported. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of TMB is 1.0

            kandi-Quality Quality

              TMB has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              TMB 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

              TMB releases are available to install and integrate.
              TMB has no build file. You will be need to create the build yourself to 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 TMB and discovered the below as its top functions. This is intended to give you an instant insight into TMB implemented functionality, and help decide if they suit your requirements.
            • Run germline calling .
            Get all kandi verified functions for this library.

            TMB Key Features

            No Key Features are available at this moment for TMB.

            TMB Examples and Code Snippets

            TMB:
            Pythondot img1Lines of Code : 19dot img1no licencesLicense : No License
            copy iconCopy
            TMB的定义如下:TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome examined. 可参考文献[1]
            
            panel size的问题对于TMB的计算很重要,不能太小,最小0.5吧,也有建议0.8以上,不过总的结论是不能太小,越大越接近外显子的结果.
            
            panel的设计初衷有时候不仅仅是call变异,也有SV、基因融合等等,  
            copy iconCopy
            根据文献[1,8]stop-gain mutations in tumor suppressor gene 应该去掉,以下两个数据库有基因的分类
            
            Oncokb database:    https://oncokb.org/cancerGenes
            
            cosmic database:    https://cancer.sanger.ac.uk/census#cl_search
              
            TMB.py,识别dbsnp已知的germline和common 位点
            Pythondot img3Lines of Code : 3dot img3no licencesLicense : No License
            copy iconCopy
            下载最新的dbsnp
            ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/
            这里的germline位点(SAO=1)和common位点(COMMON=1),这里common SNP is one that has at least one 1000Genomes population with a MAF >= 1% and for which 2 or more founders contribute to  

            Community Discussions

            QUESTION

            Cannot figure out how to combine arrays to be able to write to SQL columns in powershell
            Asked 2021-Jun-04 at 03:40

            I have been struggling with this for hours without any result :(. I have a select string command which finds various strings in the files

            ...

            ANSWER

            Answered 2021-Jun-04 at 03:40

            This should do, I'm just not sure of what the source type object types are for the variables holding the values.

            Source https://stackoverflow.com/questions/67797582

            QUESTION

            How to return string to original format after modification in JavaScript
            Asked 2021-May-16 at 21:52

            I am trying to write a sorting algorithm for sorting filesizes intelligently regardless of the input format. My function is supposed to sort an array of string inputs to give required outputs like so;

            ...

            ANSWER

            Answered 2021-May-14 at 08:29

            QUESTION

            Warning in every model of glmmTMB 'giveCsparse'
            Asked 2021-Apr-17 at 16:34

            I am using the glmmTMB library to run mixed models, within a R markdown document. Any model that I run, I get these warnings:

            ...

            ANSWER

            Answered 2021-Apr-17 at 16:34

            It's harmless. You can:

            1. ignore it
            2. use suppressWarnings() (at the possible cost of missing other relevant warnings!)
            3. install the development version from GitHub, where it was fixed in this commit. (The binary packages on the repository have also been updated now.)
            4. wait for a new version of glmmTMB to make it to CRAN (hopefully in the next few weeks ...)

            or you could downgrade your version of Matrix to an older version (using remotes::install_version() or the snapshot package)

            Source https://stackoverflow.com/questions/67040472

            QUESTION

            How can I log removed file name in elFinder with Client-event API?
            Asked 2021-Mar-23 at 15:02

            I am trying to create Ajax logging feature for elFinder so I added event handlers:

            ...

            ANSWER

            Answered 2021-Mar-23 at 15:02

            Because the path encoding method can be changed with the volume driver, the client side does not implement a function to decode it.

            However, if it is the default encoding method, it can be decoded as follows.

            Source https://stackoverflow.com/questions/66738147

            QUESTION

            Plotting an interaction with confidence intervals from an lme4 or LmerTest model in R
            Asked 2021-Mar-16 at 03:40

            Using dat (found here), I run the following model:

            ...

            ANSWER

            Answered 2021-Mar-16 at 03:40

            I'm going to answer your questions in reverse order:

            1. The plot_model() function calls functions from the ggeffects package. Specifically, ggpredict() does a lot of the work. If you go to the following URL, you will find lots of information on how to alter effects plots and getting all sorts of information from the fitted model.

            https://cran.r-project.org/web/packages/ggeffects/vignettes/ggeffects.html

            1. I don't really agree that the interaction does not look significant. The confidence interval doesn't overlap with the other categories mean for the majority of the plot. That might be beside the point, however, as you are currently plotting categorical data in a manner that makes it look continuous. This does not change how the model is being fit under the hood, but it changes the default behaviour of sjPlot. I have fit the model you specified with factors and plotted it how I think it should be plotted below. I don't think this changes much about the plot, but it might change your interpretation. The difference shown here in this plot is consistent with the model summary output and can be stated like this: the difference between the two levels of post is not the same when ess is a 0 vs. a 1. Also, see how the CIs of the two ess categories overlap with the mean when post is 0 but they are significantly different when post is 1.

            Let me know if any of this requires further clarification.

            Source https://stackoverflow.com/questions/66646449

            QUESTION

            Creating just one looping to make list - Shell
            Asked 2021-Mar-11 at 21:05

            I want to create a .xml file with an specific config, this config needs an hostname and ip, i have created the hosts.csv to input this data being them vm-tmb-test1;127.0.0.1 on .csv file for each separator line ";" is a hostname and ip of a server, but the looping i have created print for each ip in the hosts.csv

            Code Structure

            ...

            ANSWER

            Answered 2021-Mar-11 at 19:49

            A single GNU sed call could do the job:

            Source https://stackoverflow.com/questions/66589388

            QUESTION

            nodejs-slackbot - downloaded file is corrupted
            Asked 2021-Feb-19 at 13:00

            i have created a slackbot with nodejs using @slack/bolt. i'm able to receive event in my nodejs server from slack whenever i tag with my slackapp and send textMessage or textMessage+Fileattachment. Please find the nodejs source code and output of the event object below.

            The problem is, when i upload a file in slack, the event is received by my nodejs slack-bot. (shown in below screenshot+view the event object details in the output attached below)

            • The links to the uploaded file is retrieved by the nodejs slack-bot from the event object
            • i'm able to use the link in web browser(for eg. google chrome) to view the uploaded file.
            • When i use the link to download the file via nodejs code, the file gets downloaded, but the downloaded file is corrupted

            i'm not sure how to download the valid file using nodejs slack-bot. i have tried changing few parameters and settings but no success. The docs aren't helping me so far

            Please help me out

            Nodejs source code

            ...

            ANSWER

            Answered 2021-Feb-19 at 13:00
            • The issue was due to the type of token passed to the file download api
            • BOT_TOKEN is the appropriate token that has to be passed to the file download api
            • Issue got fixed once i passed the BOT_TOKEN to the file download api

            Below is the logic to download the file that was uploaded in slack

            Source https://stackoverflow.com/questions/66272475

            QUESTION

            How do I run a bash script in a server with `for` and `R` code that I can exit the terminal and does not kill the process?
            Asked 2021-Feb-09 at 20:23

            Context: I am running a simulation via R that each repetition takes too long and it is memory consuming. Therefore, I need that for every repetition another session in R starts, so that I will not run into memory issues.

            My problem: After executing my bash script, I exit from the terminal, the current repetition finishes successfully, but the next one does not start (I am running it on a server via ssh).

            What I have done:

            compoisson.sh bash script:

            ...

            ANSWER

            Answered 2021-Feb-09 at 20:23

            Solved with nohup ./compoisson.sh & instead of sh compoisson.sh &

            Source https://stackoverflow.com/questions/66103839

            QUESTION

            Program skipping if statement
            Asked 2021-Jan-28 at 11:47

            I'm a beginner with python. I've created a little program for my navigation homework which when I input the data solves it for me but it's not working. It asks the initial question to determine which type of problem to solve and then, when it's supposed to solve it, it crashes. Why is that?

            ...

            ANSWER

            Answered 2021-Jan-28 at 11:47

            Input in python receives the value as string, and you are comparing it to integer value in your if condition

            update your input statement to the following line to receive integer input:

            Source https://stackoverflow.com/questions/65936375

            QUESTION

            How to move an element into the next parent element in the DOM?
            Asked 2021-Jan-07 at 12:06

            I'm struggling to move an element into the next element in the DOM. I can move it but it keeps repeating itself into the other div's with the same class.

            This is my HTML:

            ...

            ANSWER

            Answered 2021-Jan-07 at 12:06

            To achieve this you could loop through all p elements as there are multiple, and then use appendTo() to add them to their related .tmb. Try this:

            Source https://stackoverflow.com/questions/65611988

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

            Vulnerabilities

            No vulnerabilities reported

            Install TMB

            You can download it from GitHub.
            You can use TMB 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

            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://github.com/fanyucai1/TMB.git

          • CLI

            gh repo clone fanyucai1/TMB

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            git@github.com:fanyucai1/TMB.git

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