arriba | Fast and accurate gene fusion detection from RNA-Seq data | Genomics library
kandi X-RAY | arriba Summary
kandi X-RAY | arriba Summary
Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. It is based on the ultrafast STAR aligner, and the post-alignment runtime is typically just ~2 minutes. Arriba's workflow produces fully reusable alignments, which can serve as input to other common analyses, such as quantification of gene expression. In contrast to many other fusion detection tools which build on STAR, Arriba does not require to reduce the STAR parameter --alignIntronMax to detect fusions arising from focal deletions. Reducing this parameter impairs mapping of reads to genes with long introns and may affect expression quantification, hence. Apart from gene fusions, Arriba can detect other structural rearrangements with potential clinical relevance, including viral integration sites, internal tandem duplications, whole exon duplications, intragenic inversions, enhancer hijacking events involving immunoglobulin/T-cell receptor loci, translocations affecting genes with many paralogs such as DUX4, and truncations of genes (i.e., breakpoints in introns or intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge, an international competition organized by ICGC, TCGA, IBM, and Sage Bionetworks to determine the current gold standard for the detection of gene fusions from RNA-Seq data. The final results of the challenge are posted on the Round 5 Leaderboard and discussed in the accompanying publication.
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QUESTION
ANSWER
Answered 2021-May-27 at 01:28I suggest you should extract new column from lugar column like below code.
QUESTION
I am making a form in which once I fill in the data I validate them through regular expressions they can be sent.
I have also created a JavaScript file that calls a JSON to enter the marital status of a person, the thing is that in that file in the function that I have to be able to validate, send the data or delete or display it, I get that error, and no matter how many changes you make, it doesn't stop appearing.
Here I pass the error and the code in question.
...
ANSWER
Answered 2021-May-24 at 14:37There were 2 (or perhaps 3) problems with your code
- Don't use
evalsetxmlhttp.responseType = "json"and just read theresponsedirectly. - You were not reading the
estado_civilproperty of the returned object - The properties you were trying to read did not exist on the returned object.
I have fixed all 3 below how I think you intended it to work.
QUESTION
Trying to configure a basic color detection in my ROS project, I got stuck in this: I have two python scripts where "programa.py" is my main robot program and the "camara.py" is my openCV color detection script.
Right now I can change the color detection publishing a string message when camara.py is running:
...ANSWER
Answered 2020-Dec-11 at 17:51You can write a publisher for that.
Define a publiser in your init
QUESTION
Hello I'm working on a cashier like app, I've created my menu and buttons, however I would like to add specific functionality to my Jbuttons, I've read a lot of questions related to this here but unfortunately I've not come up with a solution, I would like to know how could I possibly add some variable managment or image changing function to my Jbuttons
...ANSWER
Answered 2020-Nov-29 at 19:54QUESTION
My goal is to remove from df11 dictionary, every 'update_timestamp' subdictionary. Note that in some of the sub-dictionaries (for example in 2 and 3) 'update_timestamp' doesn't exist.
This is what I have tried in order to remove them:
...ANSWER
Answered 2020-Nov-14 at 00:46This should do the job. not so efficient but working.
QUESTION
I'm trying to do a basic nav-bar. This nav bar contains a "search" button.
My goal is to make a hover in the search button that makes appear an input (and moves the button to the left) for the user to search anything he wants.
The thing is: I need to make the search button move to the left when I hover the input too, and I'm not figuring it out.
And as you see with that code, the item bugs.
Here's the code:
...ANSWER
Answered 2020-Oct-25 at 06:25Answer: Onclick javascript statement added...
QUESTION
I have to make a Tictactoe for a project, and while i do know that the code is not good, i can´t see what the error is, the value is assigned to the dict, if i print the key for the last play its correctly show me if is an X or a O, but the value is not represented in the last print of the board.
...ANSWER
Answered 2020-Oct-22 at 14:43You are assigning the new X or O to tablero['algo']. If the game doesn't end here, you assign the contents of tablero to ari, arc, etc., but only at the start of the next loop.
So if the game does end after that move, you print the old ari, arc, etc. which have not yet been updated to reflect the latest move.
Of course, there are many other things you should fix (lots of repetition that can be avoided), but the game does work correctly.
Some suggestions:
I would use a simple list to handle the board. tablero = [" "] * 9 creates a list of nine space characters. This allows for a lot of simplications down the line. For example, to print the board, you can simply do
QUESTION
I have a script in PHP where i'm defining the menus and navbars of the website. I have a top menu that when you scroll down the page, it gets fixed to the top of the page. I want to have a second menu on the left "glued" to the top menu. The way I have done it, it goes well when the top menu reaches the top of the page, it gets fixed with the left menu like I want. The problem is that if the top menu doesnt reach the top of the page (like if it's just a little bit of scroll), the left menu doesnt get stick to the top menu.
The top menu is the one that has "Inicio", "Instrucciones" etc. The left menu is the one that has "Nueva cata", "Nueva cerveza", etc.
This is the page at the beginning (0 scroll).
This is the page after the top menu reaches the top of the page (>200 scroll).
This is the page before the top menu reaches the top of the page (0 < scroll < 200).
As you can see in the third page, the left menu goes down with the scroll instead of going up with the top menu.
This is HTML:
...ANSWER
Answered 2020-Jul-25 at 15:40Looks like you are using Bootstrap. Currently, your left nav is initially set to position: fixed, I recommend using position: relative to your left nav initially so that positioning your nav elements can be relative to the height of the background image. Using Bootstrap, this solution wraps the left nav & the content in a flex container so that the content can be positioned relative to this container easily, since later on the navs are going to get position: fixed.
Basically on the script, just detect if the top of the scroll bar's Y position is already past the height of the background image element. If it is, assign the fixed position to the nav elements and adjust the content's position as needed relative to the container wrapping the left nav & the content. Check the CSS properties involving .navs-are-fixed to see how the navs are assigned the fixed position.
QUESTION
I have an 1000x1000px image which I want to divide into 10x10 px squares. I have the variable "coordenada" to track the coords of the current 10x10 square (that's why when trying to get the x and y values I multiply by 10).
I want to draw a rectangle surrounding the "current" 10x10 square given by the coords. I get corner 1 (p1) by multiplying the coords by 10 and corner 2 (p2) by doing the same and adding 10. I want the color of the frame to be the same as the color it has in the middle of the square, so I access that color using canvas[x, y], canvas being the name of the image loaded in a numpy array, and typecasting it into a tuple since that is what I read I need to send cv.rectangle. This is the resulting code (minus declaration of canvas and coordenada):
...ANSWER
Answered 2020-Jul-19 at 23:42The error message seems misleading -- it looks like the TypeError stems from colorOfFrame tuple not consisting of int elements (it consists of np.uint8's).
You can avoid the error by explicitly casting pixel values to int. Here is one way to do this:
QUESTION
I am trying to make a game on javascript. In Computer version it works correctly, but when I try to prove in mobile version (Google chrome > F12 > Toggle device toolbar or Ctrl+Shift+M), game is lagging at tap the left/right bottoms.
I have tried to change div elements to buttoms, but really I dont know where is the problem. It is not a complex game, or at least I think.
Here is the code:
...ANSWER
Answered 2020-May-17 at 12:15This also happened to me and I had no idea what the problem was. I submitted a bug report to the Chrome team, and the response was the following:
I believe this is expected. If you add an event listener, a touchstart may indicate that scrolling is about to happen (Chrome can't tell a priori whether the event will be preventDefaulted). We thus avoid scheduling any Javascript tasks like timers to ensure touch handlers remain responsive so the potential upcoming scroll can start ASAP.
So, basically, Chrome stops timers for a bit of time after the user begins touching the screen to ensure responsiveness in scrolling.
There are two easy ways to avoid this:
-
This is a promise to Chrome that the handler doesn't call
ev.preventDefault()so we can tell ahead of time that a touch drag will cause scrolling. Because of that, when we're ready to scroll (off the Javascript thread) we don't have to wait for handlers to respond and we can scroll immediately, so we don't have to keep the JS thread idle to get responsiveness.
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