tracer | cell receptor sequences from single-cell RNAseq data | Genomics library
kandi X-RAY | tracer Summary
kandi X-RAY | tracer Summary
This tool reconstructs the sequences of rearranged and expressed T cell receptor genes from single-cell RNA-seq data. It then uses the TCR sequences to identify cells that have the same receptor sequences and so derive from the same original clonally-expanded cell. For more information on TraCeR, its validation and how it can be applied to investigate T cell populations during infection, see our paper in Nature Methods or the bioRxiv preprint that preceded it. Please email questions / problems to mjt.stubbington [at] gmail.com.
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Top functions reviewed by kandi - BETA
- Run plot
- Return the number of recombination for a given receptor and locus
- Returns a list of unique identifiers for a given receptor
- Count the number of recombins for a given receptor and locus
- Generates a networkx graph for each cell
- Generate a networkx graph from a DNA sequence
- Return HTML for the contour
- Return HTML for dna label dna
- Run build
- Calculate the colour map for a given colour
- Copy the raw sequence files for each strain
- Advance v
- Perform TraCeE
- Alignment with bowtie2
- Remove duplicates from the recombination
- This function is called by de unovo
- Run assembly
- Returns the path to tracer
- Run an expression quantification
- Return a FASTA string
- Read config file
- Launch TraCeR
- Run quantify expression quantification
tracer Key Features
tracer Examples and Code Snippets
Lines of Code : 93License : Non-SPDX (Apache License 2.0)
Copydef set_parameters(tensor_tracer_params=None):
"""Enables tensor tracer and sets its parameters.
Example usage:
tensor_tracer_parameters = {'trace_dir': '/usr/tmp/trace_dir',
'trace_mode': 'norm',
Community Discussions
Trending Discussions on tracer
QUESTION
I would like to display all my traces like in the examples from the moleculer-jaeger package:
But what i get is something like this: All spans you can see in this picture should be within the main trace (gateway).
Here is my moleculer.config:
...ANSWER
Answered 2021-Jun-14 at 21:33- This version already has a built-in jager tracer, see the documentation.
- In order for the events to be nested, it is necessary to transfer the context inside the actions, use
ctx.callcalls instead ofbroker.call, so they will be nested. - To quickly receive support for the moleculer, join us in discord!
QUESTION
I want to make the yellow block jump on the line when there are other shapes. Also, how could I make the screen to close when the yellow block touches the other blocks.
I have though about using the time module and put time.sleep for 1 seconds after blockself.goto(0,30) then make the block go down to (0,0). However, when I did that the whole screen frozed for 1 second. This means that the time.sleep was not aimed for the blockself(yellow block) it self. Is there any way to fix this.
ANSWER
Answered 2021-Jun-13 at 02:33We can make the yellow block vertical jump independent of the other motion using the same mechanism I gave you for the horizontal block motion, ontimer(). The jump() method below is invoked by the keyboard event, moving the yellow block up and down as a series of timer events:
QUESTION
Let say I have a matrix W of shape (n_words, model_dim) where n_words is the number of words in a sentence and model_dim is the dimension of the space where the word vectors are represented. What is the fastest way to compute the moving average of these vectors ?
For example, with a window size of 2 (window length = 5), I could have something like this (which raises an error TypeError: JAX 'Tracer' objects do not support item assignment):
ANSWER
Answered 2021-Jun-09 at 16:50This looks like you're trying to do a convolution, so jnp.convolve or similar would likely be a more performant approach.
That said, your example is a bit strange because n is never larger than 4, so you never access any but the first four elements of W. Also, you overwrite the previous value in each iteration of the inner loop, so each row of new_W just contained a scaled copy of one of the first four rows of W.
Changing your code to what I think you meant and using index_update to make it compatible with JAX's immutable arrays gives this:
QUESTION
Copying a VkImage that is being used to render to an offscreen framebuffer gives a black image.
When using a rasterizer the rendered image is non-empty but as soon as I switch to ray tracing the output image is empty:
...ANSWER
Answered 2021-Jun-06 at 09:08Resolved by now:
When submitting the command buffer to the queue it would require an additional vkQueueWaitIdle(m_queue) since ray tracing finishes with a certain latency
QUESTION
Open Telemetry InMemorySpanExporter not resetting after test class is complete. This is causing span_list = self.memory_exporter.get_finished_spans() to be empty for the 2nd test class.
ANSWER
Answered 2021-Jun-03 at 19:32Your description was not clear but I can share why you are running into AssertionError. This is happening because we don't allow setting global tracer provider once it is already set; link to code which does that. There can only be one global tracer provider. So, when the call to trace.set_tracer_provider made in second test it logs warning without doing anything hence your second attempt to set pipeline was unsuccessful i.e second exporter never received the spans.
QUESTION
I am trying to make a Pong game and as you can see in the screenshot ( at the end of this question ), In the right hand side I have created a paddle.
Everything works fine in following code, when I press Up and Down arrows, the paddle moves up and down.
Kindly note placement of statement “ screen.update()”
...ANSWER
Answered 2021-Jun-03 at 15:41Why is my code not working in SECOND CASE
Because you haven't put a screen.update() everywhere you make a change that you want the user to see. Specifically the go_up() and go_down() methods:
QUESTION
I thought using Screen.tracer(0) disabled animation in Python Turtle Graphics. However in the following program, if you comment out screen.update(), there is still some animation happening - the turtle trail gets drawn although the turtle doesn't "move" (or get updated). What is happening here please? Is there way to make updating the screen completely manual?
ANSWER
Answered 2021-Jun-02 at 18:26No, screen.tracer(0) doesn't stop all animation. Some turtle commands like end_fill() invoke screen.update() directly, some like dot() invoke it due to other methods that they in turn invoke. You only advise the system when you call update(), not control it completely.
Put your update() calls where you believe you need them, and don't assume certain methods force an update, otherwise future updates of turtle might break your code. (I.e. someone might actually fix turtle.)
For potentially helpful details, see my tracer() rules of thumb and information about the first argument's numeric value
QUESTION
The following code does not work:
...ANSWER
Answered 2021-May-30 at 03:49No, for the reasons you mention, there's currently no way to use jnp.unique on a non-static value.
In similar cases, JAX sometimes adds extra parameters that can be used to specify a static size for the output (for example, the size parameter in jax.numpy.nonzero) but nothing like that is currently implemented for jnp.unique. If that is something you'd like, it would be worth filing a feature request.
QUESTION
I'm making a sequential request using Feign Builder. There are no x-b3-traceid,x-b3-spanid .. in the title of the request. That's why the log my last client appears on the zipkin.
I use spring boot 2.4.2 , spring cloud 2020.0.0 , feign-core 10.10.1 , feign-okhttp 10.10.1. I have tried spring-cloud-openfeign and i achieved wanted result. But i don't want to use this lib. There are requests when using Feign Builder and Rest Template in here. I dont' see same log at zipkin.
My Client1 App. I am sending request http://localhost:8082/
...ANSWER
Answered 2021-Mar-01 at 08:16The problem might be related to the fact that you're creating the Feign builder manually via Feign.builder() factory method. We're unable to instrument that call. You should create a bean (via SleuthFeignBuilder.builder) and inject that into your code.
QUESTION
I've been testing the turtle library for about 3 days now. One recurring 'issue' that I've been getting is the traceback error whenever I exit my application window. The terminal displays rows of details regarding the turtle update function and it ends with:
...ANSWER
Answered 2021-May-26 at 19:07The problem is your loop:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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Install tracer
To set up the python dependencies, use the requirements file:. It is highly recommended that numpy and biopython are first installed through your system's package manager or conda.
The -c option used at run time for any of the TraCeR modes
The environmental variable TRACER_CONF, which can be set to point to a default location
The default global location of ~/.tracerrc
If all else fails, the provided example tracer.conf in the directory is used
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