hic | Analysis of Chromosome Conformation Capture data | Genomics library

 by   nf-core Python Version: 1.3.0 License: MIT

kandi X-RAY | hic Summary

kandi X-RAY | hic Summary

hic is a Python library typically used in Artificial Intelligence, Genomics applications. hic has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However hic build file is not available. You can download it from GitHub.

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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            kandi-support Support

              hic has a low active ecosystem.
              It has 43 star(s) with 35 fork(s). There are 84 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 24 open issues and 38 have been closed. On average issues are closed in 190 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of hic is 1.3.0

            kandi-Quality Quality

              hic has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              hic is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              hic releases are available to install and integrate.
              hic has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed hic and discovered the below as its top functions. This is intended to give you an instant insight into hic implemented functionality, and help decide if they suit your requirements.
            • 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
            Get all kandi verified functions for this library.

            hic Key Features

            No Key Features are available at this moment for hic.

            hic Examples and Code Snippets

            No Code Snippets are available at this moment for hic.

            Community Discussions

            QUESTION

            Make a flex item grow at hover without affecting the other flex elements
            Asked 2021-Jun-14 at 14:29

            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 11:42

            Apply align-items property so that flex children doesn't stretch:

            Source https://stackoverflow.com/questions/67957790

            QUESTION

            Expected BEGIN_OBJECT but was BEGIN_ARRAY but the json respone has already an object
            Asked 2021-Jun-13 at 08:32

            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 06:45

            You are using the wrong model. according to your json output, your model must be the below classes

            Source https://stackoverflow.com/questions/67955557

            QUESTION

            React-Router rendering props
            Asked 2021-Jun-10 at 15:24

            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 15:24
            Issue

            The introduction prop isn't passed to the Article component rendered by the Route in your main router in App.

            Source https://stackoverflow.com/questions/67923624

            QUESTION

            How to use jquery to achieve the switching effect of jump
            Asked 2021-Jun-10 at 02:56

            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 02:56

            Although 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.

            Source https://stackoverflow.com/questions/67908465

            QUESTION

            How to use jquery or CSS to display the blue block after touching the yellow block?
            Asked 2021-Jun-09 at 08:16

            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 08:16

            When the mouse touches the yellow block, the blue block will be displayed and return to the displayed height.

            Just add the following jquery :

            Source https://stackoverflow.com/questions/67899534

            QUESTION

            Navbar not filling width of page when reduced to mobile view
            Asked 2021-Jun-03 at 18:40

            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 18:40

            Probably 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.

            Source https://stackoverflow.com/questions/67826504

            QUESTION

            Link color is not changing after adding a class with jQuery
            Asked 2021-Jun-03 at 11:47

            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 11:47

            Use the class like this:

            Source https://stackoverflow.com/questions/67820303

            QUESTION

            Footer not staying at the bottom when scrolling
            Asked 2021-Jun-03 at 11:35

            ...

            ANSWER

            Answered 2021-Jun-03 at 11:35

            QUESTION

            How to properly do JSON API GET requests and assign output (Kimai Time Tracking)
            Asked 2021-May-28 at 11:45

            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 11:45

            You could use the HttpClient API to issue a REST request and then parse the response directly in your .NET app:

            Source https://stackoverflow.com/questions/67737198

            QUESTION

            Lumen/Laravel: sum on nested relationships
            Asked 2021-May-28 at 09:47

            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 09:47

            On your Procedure model, as documentFiles as a hasManyThrough relation.

            Source https://stackoverflow.com/questions/67736481

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

            Vulnerabilities

            No vulnerabilities reported

            Install hic

            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. 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.
            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

            Support

            The nf-core/hic pipeline comes with documentation about the pipeline: usage and output. For further information or help, don't hesitate to get in touch on Slack. You can join with this invite.
            Find more information at:

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