DENDRO | Genetic Heterogeneity Profiling by Single Cell RNA | Genomics library

 by   zhouzilu R Version: v0.2.1 License: GPL-3.0

kandi X-RAY | DENDRO Summary

kandi X-RAY | DENDRO Summary

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

This DENDRO package includes two analysis tools: (1) DENDRO, a phylogenetic tree construction with real dataset such as tumor and hematopoesis scRNA-seq, and (2) DENDROplan, which help design experiment by predicting the accuracy of DENDRO cluster given inferred clonal tree structure, cell number and sequencing depth. Overall pipelines are shown below.
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              DENDRO has a low active ecosystem.
              It has 16 star(s) with 5 fork(s). There are 1 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 10 open issues and 4 have been closed. On average issues are closed in 133 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of DENDRO is v0.2.1

            kandi-Quality Quality

              DENDRO has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              DENDRO is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

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

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            DENDRO Key Features

            No Key Features are available at this moment for DENDRO.

            DENDRO Examples and Code Snippets

            No Code Snippets are available at this moment for DENDRO.

            Community Discussions

            QUESTION

            How to plot DENDROGRAM in GUI
            Asked 2021-Feb-27 at 16:21

            I am using a GUI from QtDesigner to plot Dendrogram. My code is below, but I can not plot the Dendrogram, how can I fix it?

            ...

            ANSWER

            Answered 2021-Feb-27 at 10:18

            You have to import the dendrogram from scipy:

            Source https://stackoverflow.com/questions/66397433

            QUESTION

            How to get a readable scale on a particular R plot?
            Asked 2020-Aug-11 at 08:50

            I already made a post for this question on biostars forum (https://www.biostars.org/p/452352/) but did not get a lot of replies.

            I'm having difficulties to get a plot with a readable scale.

            I have plotted transcriptomic data using R with package EMA. However 'genes names' (ordinate axis) are written too big and I can't see all gene names. I would like to have one gene name per compartment.

            Here is my code:

            ...

            ANSWER

            Answered 2020-Aug-03 at 09:51

            As a workaround you could follow this tutorial by Dave Tang:

            Source https://stackoverflow.com/questions/63225729

            QUESTION

            how to keep samples in valid clusters?
            Asked 2019-Dec-09 at 13:26

            I have 72 sample in my datExprSTLMS as gene expression dataset and ran clustering on this data set based on below code:

            ...

            ANSWER

            Answered 2019-Dec-09 at 13:26

            Change keepSamples = (Cutreecluster_Sample==!0) to keepSamples = (Cutreecluster_Sample!=0)

            Why? Evaluating your command from right to left: !0 is a logical negation of 0, which is equivalent to !FALSE in R. Thus !0 is equal to TRUE. You then check if Cutreecluster_Sample equals TRUE. TRUE coerced to numeric is 1 in R. Thus your check is actually TRUE iff samples are in cluster 1, not cluster 0.

            Try !0 == 1 and FALSE == 0.

            Source https://stackoverflow.com/questions/59249753

            QUESTION

            How to save a scipy dendrogram as high resolution file?
            Asked 2019-Oct-22 at 14:29

            I have a matrix which has 600 different labels. Therefore, it is really big file; and I couldn't see these labels very well, when I created a figure to cluster my data. How should I create a high resolution file and save it?

            I already tried below code.

            ...

            ANSWER

            Answered 2019-Oct-22 at 14:29

            The problem is not with your resolution, but the size of the image (or the size of the lines). Since i do not know how to change the linewidth in the dendogram plot, i will just go with the straight forward solution to make a HUGE image.

            Source https://stackoverflow.com/questions/58495420

            QUESTION

            Ordering heatmap rows by labRow
            Asked 2019-Sep-27 at 15:53

            I've got a heatmap from a FoldChange dataset (176x10) and labeled it using another data.frame (176x2) where I have only the genes (rownames of the main dataset) and their resulting protein abreviation.

            Although there are different 176 genes, most of them results in the same protein so I have 22 different abreviations (row labels).

            I would like to group the rows by the protein abreviations.

            This is the code I'm running, where teste is the main data.frame and ident is the identification data.frame:

            ...

            ANSWER

            Answered 2019-Sep-27 at 15:53

            As mentioned in my comment, you can do this quite easily by ggplot2 facetting. Here's a rough example.

            Source https://stackoverflow.com/questions/57857389

            QUESTION

            Color labels of ggdendro plot
            Asked 2019-Feb-11 at 09:21

            I am trying to apply dendextend in order to color the ggdendro labels. I get this error:

            ...

            ANSWER

            Answered 2019-Feb-11 at 08:46

            Seems you were confusing dendrogram with dendrogram data. This will work:

            Source https://stackoverflow.com/questions/54616539

            QUESTION

            R: display clustered heatmap with simlarity matrix
            Asked 2017-Oct-28 at 20:09

            I have a simlarity matrix as follows:

            ...

            ANSWER

            Answered 2017-Oct-28 at 20:09

            I have figured it out upon reading one of the examples in R. Here is what one has to do using the similarity matrix.

            Source https://stackoverflow.com/questions/46986116

            QUESTION

            How to use bindings in controller in an AngularJs 1.6 component
            Asked 2017-Oct-23 at 07:30

            Hello here is my component :

            ...

            ANSWER

            Answered 2017-Oct-22 at 12:38

            From the documentation:

            Components have a well-defined lifecycle Each component can implement "lifecycle hooks". These are methods that will be called at certain points in the life of the component. The following hook methods can be implemented:

            • $onInit() - Called on each controller after all the controllers on an element have been constructed and had their bindings initialized (and before the pre & post linking functions for the directives on this element). This is a good place to put initialization code for your controller.
            • $onChanges(changesObj) - Called whenever one-way bindings are updated. The changesObj is a hash whose keys are the names of the bound properties that have changed, and the values are an object of the form

            So you can just use:

            Source https://stackoverflow.com/questions/46874031

            QUESTION

            R: how to count the number of times two elements have the same ID (perhaps using the outer function)
            Asked 2017-Oct-17 at 13:41

            I have the following three dimensional array:

            ...

            ANSWER

            Answered 2017-Oct-17 at 05:09

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

            Vulnerabilities

            No vulnerabilities reported

            Install DENDRO

            Install to R/RStudio Install all packages in the latest version of R. If you observe error with Biobase try the following and then try reinstall.

            Support

            If you have any questions or problems when using DENDRO or DENDROplan, please feel free to open a new issue here. You can also email the maintainers of the corresponding packages -- the contact information is shown under Developers & Maintainers.
            Find more information at:

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            https://github.com/zhouzilu/DENDRO.git

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            gh repo clone zhouzilu/DENDRO

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            git@github.com:zhouzilu/DENDRO.git

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