hic | Analysis of Chromosome Conformation Capture data | Genomics library
kandi X-RAY | hic Summary
kandi X-RAY | hic Summary
This pipeline was originally set up from the HiC-Pro workflow. It was designed to process Hi-C data from raw FastQ files (paired-end Illumina data) to normalized contact maps. The current version supports most protocols, including digestion protocols as well as protocols that do not require restriction enzymes such as DNase Hi-C. In practice, this workflow was successfully applied to many data-sets including dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip data. Contact maps are generated in standard formats including HiC-Pro, and cooler for downstream analysis and visualization. Addition analysis steps such as compartments and TADs calling are also available. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
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Top functions reviewed by kandi - BETA
- Determine the interaction type of two RNA sequences
- Return the reads ordered by position
- Get the read position of a read
- Return True if two reads are dangling
- Calculate the contact distance between two reads
- Checks if two reads are an intra chromosome
- Convert a markdown file to HTML
- Replace N
- Compares two reads
- Print timing information
- Parse command line arguments
- Get command line arguments
- Find chromosome names and lengths
- Return the size of the PE fragment in the read2
- Print usage information
- Get the orientation of two reads
- Check if the restriction fragments overlap with the given chromosome
- Wrap html
- Find re - sites in a file
- Convert s to int
hic Key Features
hic Examples and Code Snippets
Community Discussions
Trending Discussions on hic
QUESTION
I have box elements in a flex container. I want the paragraph in a box to display when hovering over the box. However, the hovered box makes the other boxes grow too. Is there a way to avoid affecting the other boxes when hovering one box?
I would try: align-items:flex-start, but I want the boxes to be equivalent in height when they are not hovered.
So align-items:flex-start does not keep the boxes' height equivalent when they are not hovered.
I want the box to enlarge when hovered without affecting the other boxes and turn back to the equivalent height when not hovered.
Codepen link: https://codepen.io/lemour-sudo/pen/yLMQOpE
...ANSWER
Answered 2021-Jun-13 at 11:42Apply align-items
property so that flex children doesn't stretch:
QUESTION
I am learning retrofit 2 and got an error like this :
W/System.err: com.google.gson.JsonSyntaxException: java.lang.IllegalStateException: Expected BEGIN_OBJECT but was BEGIN_ARRAY at line 1 column 94 path $.riceField at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.read(ReflectiveTypeAdapterFactory.java:226) at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$1.read(ReflectiveTypeAdapterFactory.java:131) at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.read(ReflectiveTypeAdapterFactory.java:222) at retrofit2.converter.gson.GsonResponseBodyConverter.convert(GsonResponseBodyConverter.java:40) at retrofit2.converter.gson.GsonResponseBodyConverter.convert(GsonResponseBodyConverter.java:27)
and here is the code
api
...ANSWER
Answered 2021-Jun-13 at 06:45You are using the wrong model. according to your json output, your model must be the below classes
QUESTION
I'm using react router for my project and I need to render separate props (the introduction) to another component which is accessible through my Card component. Currently, each card has a title of a blog, when the "Read more" button is clicked , I want the article page to render showing the introduction for each blog, but nothing is showing.
Blog
...ANSWER
Answered 2021-Jun-10 at 15:24The introduction
prop isn't passed to the Article
component rendered by the Route
in your main router in App
.
QUESTION
I have a problem but my thoughts are knotted, I want to get help here!
"Requirement"
when the mouse hoveres to the yellow block, the blue block should be slowly slid down from its original place. When the mouse leaves, the blue block can be slowly folded upwards.
I don’t know how to write it here, it’s easier?
Thank you everyone for watching my question, and thank you again.
...ANSWER
Answered 2021-Jun-10 at 02:56Although it's not jquery I think it does what you want. Your button placement cause the blue and yellow divs to go beyond the screen because of your padding. You'll want to clean that up. You can change the transition times and also have different times by not using all
but rather listed opacity
and height
separalty.
QUESTION
I would like to ask you a question. I hope that when the yellow block is displayed, when the mouse hovers over the yellow block stone, the original blue block can be displayed again!
But I still can't achieve the effect after trying it for an afternoon. Would you like to ask everyone to help me see if there is a problem? Thank you all for your help.
...ANSWER
Answered 2021-Jun-09 at 08:16When the mouse touches the yellow block, the blue block will be displayed and return to the displayed height.
Just add the following jquery :
QUESTION
Screenshot of problem hereThis is my first post to stackoverflow so go easy on me if I am not doing something right haha.
I'm working on my project for a course I am doing. It's with Bootstrap 4 and the issue I am having is the navbar when being resized starts to lose it's full width. My guess is the content beneath it was causing this but I am not sure how I go about fixing it.
I really would appreciate any guidance here as it's been driving me mental and I know it's possibly somthing so easy but I can't spot what I am doing wrong.
Thanks in advance look forward to chatting.
Mike
...ANSWER
Answered 2021-Jun-03 at 18:40Probably because your .card-about
width is wider than your viewport.
Try using max-width
instead so. I changed your height
into auto
so the content wont overflow when the height become bigger.
QUESTION
I am a beginner. I am trying to make a webpage. But I'm having a problem. I added a class with the help of jQuery so that the background color(white) of the navbar changes when scrolling. I also want to change the color of the link in the navbar so that it can be visible after adding the navbar background color(white) because the navbar links color is white. Scrolling changes the background color of the navbar but not the color of the link.
...ANSWER
Answered 2021-Jun-03 at 11:47Use the class like this:
QUESTION
ANSWER
Answered 2021-Jun-03 at 11:35EDIT change to this:
QUESTION
I want to write a simple desktop application to track the overtime work of our employees. Whenever one of our employees needs to perform some tasks outside our normal working hours we want to track them using "Kimai Time Tracking".
The application I am programming needs to get the duration of all recorded tasks from Kimai, add them up and store them on a local SQL Server as an overtime contingent for the employee to claim later.
This is the GET request I'm mainly gonna use:
GET /api/timesheets (Returns a collection of timesheet records)
and this is an example output from the Kimai Demo (Sorry for length)
...ANSWER
Answered 2021-May-28 at 11:45You could use the HttpClient API to issue a REST request and then parse the response directly in your .NET app:
QUESTION
i've got these nested relationship in Lumen 8, i'm looking for a well-done Eloquent way to show the sum of files size, but on relation father level. That's my situation:
Procedures ->(hasMany) Documents ->(hasMany) DocumentFiles
I want to sum DocumentFiles->size but on Procedure. (field procedure_files_size) If possible i would like to show the sum also for the single document. (field document_files_size)
That's like what i'm expecting to have when returning the Procedure Object:
...ANSWER
Answered 2021-May-28 at 09:47On your Procedure
model, as documentFiles
as a hasManyThrough
relation.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install hic
Install nextflow (>=20.04.0)
Install any of Docker, Singularity, Podman, Shifter or Charliecloud for full pipeline reproducibility (please only use Conda as a last resort; see docs)
Download the pipeline and test it on a minimal dataset with a single command nextflow run nf-core/hic -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute> Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.
Start running your own analysis! nextflow run nf-core/hic -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
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