Juicebox | Visualization and analysis software for Hi-C data | Genomics library
kandi X-RAY | Juicebox Summary
kandi X-RAY | Juicebox Summary
Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files. Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website for more details on how to use Juicebox for assembly. Juicebox was created by Jim Robinson, Neva C. Durand, and Erez Lieberman Aiden. Past contributors include Ido Machol, Zulkifl Gire, Marie Hoeger, Fanny Huang, Nam Hee Kim, Vi Nguyen, Jay Ryu, Nathaniel T. Musial, and Ragib Mostofa. Ongoing development work is carried out by Muhammad Saad Shamim, Neva C. Durand, and Olga Dudchenko.
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
- Creates the menu items
- Scales the iterator to the target vector
- Safely loads the state of the map
- Computes the expected value calculation
- Performs the localizer
- Order peaks in the expected data
- Calculates local maximum number of contacts in the local matrix
- Initialize reload colors
- This method is called when an action button is pressed
- Called when mouse is pressed
- Write normalized sum
- Updates a hi - coordinate vector
- Runs the demo
- Renders a track panel
- Main loop
- Initialize the components
- Writes the body to the file
- Paint the component
- Draws the component
- Generates a list of peaks for the given input
- Called when the mouse is pressed
- Creates the cursors
- Handle mouse move event
- Returns true if false
- This method is used to run the CPU kernel
- Called when the popup is pressed
Juicebox Key Features
Juicebox Examples and Code Snippets
Community Discussions
Trending Discussions on Juicebox
QUESTION
I'm trying to use a list of phrases (over 100) which I want to be removed from a text file (products.txt) which has lines of text inside it (they are tab separated / new line each). So that the results which do not match the list of phrases will be re-written in the current file.
...ANSWER
Answered 2020-Dec-26 at 19:43here's one way to do what you want. it's somewhat more direct than what yo used. [grin] it uses the way that PoSh can act on an entire collection when it is on the LEFT side of an operator.
what it does ...
- fakes reading in a text file
when ready to do this in real life, replace the whole#region/#endregionblock with a call toGet-Content. - builds the exclude list
- converts that into a regex OR pattern
- filters out the items that match the unwanted list
- shows that resulting list
the code ...
QUESTION
I'm making a JavaScript Module that imports a popup box and the import doesn't seem to work. I need some help making my javascript program work
...ANSWER
Answered 2020-Oct-03 at 09:47There are two problems:
You can't use
importin a script, only in a module. To indicate your inline code is a module, you need to addtype="module"to thescripttag:
QUESTION
Is there a function to find the input handlers for a package, generally? There are several special input handlers for leaflet, e.g. input$mymap_shape_mouseover that are not anywhere listed in the R documentation. Really, I just want to be able to grab the coordinates of a flat png heatmap that I'm using with leaflet and reformat them to grab the coordinates in the matrix I've previously plotted.
...ANSWER
Answered 2018-Apr-17 at 21:01For those interested in leaflet input events - such as input$MAPID_center - please thank @blondclover. They recommended a nifty trick to print out all input events:
- Create the
output$outputIDin the UI usingverbatimTextOutput; and - Store the results of
renderPrint({reactiveValuesToList(input)})in theoutput$outputIDobject in server.
As the complexity of your leaflet map grows, knowing which leaflet input events are available to use will help you customize your map.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install Juicebox
Then go to VCS -> checkout from version control.
You'll need to do is be sure *.sizes is included as a file to be copied over to the class files. Set this up via IntelliJ Preferences -> Compiler. Add ?*.sizes to the list of Resource Patterns.
While there, also go to Java Compiler and put this into additional command line options: -Xlint:all -target 1.7 The former turns on all warnings, the latter gives some flexibility since some people haven't updated Java to 1.8 yet.
Then go to Run -> Edit Configurations.
With the + sign, add Application.
You'll create two of these, one for the GUI (call it Juicebox GUI or whatever you want, really) and one for the CLT.
Set the main class by clicking the little ... button next to the text box for main class MainWindow.java is the main method class for the visualization/GUI portion of the software. HiCTools.java is the main method class for the analysis/CLT portion.
For the GUI under VM Options: -Xmx2000m -Djnlp.loadMenu="https://hicfiles.tc4ga.com/juicebox.properties"
For the CLT use -Xmx2000m
Note that the Xmx2000m flag sets the maximum memory heap size to 2GB. Depending on your computer you might want more or less. Some tools will break if there's not enough memory and the file is too large, but don't worry about that for development; 2GB should be fine.
One last note: be sure to Commit and Push when you commit files, it's hidden in the dropdown menu button in the commit window.
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page
