MACS | MACS -- Model-based Analysis of ChIP-Seq | Genomics library

 by   macs3-project Python Version: v3.0.0a6 License: BSD-3-Clause

kandi X-RAY | MACS Summary

kandi X-RAY | MACS Summary

MACS is a Python library typically used in Artificial Intelligence, Genomics applications. MACS has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install MACS' or download it from GitHub, PyPI.

With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we presented the Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with a control sample with the increase of specificity. Moreover, as a general peak-caller, MACS can also be applied to any "DNA enrichment assays" if the question to be asked is simply: where we can find significant reads coverage than the random background.
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            kandi-support Support

              MACS has a low active ecosystem.
              It has 488 star(s) with 223 fork(s). There are 56 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 200 open issues and 189 have been closed. On average issues are closed in 46 days. There are 2 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of MACS is v3.0.0a6

            kandi-Quality Quality

              MACS has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              MACS is licensed under the BSD-3-Clause License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              MACS releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed MACS and discovered the below as its top functions. This is intended to give you an instant insight into MACS implemented functionality, and help decide if they suit your requirements.
            • Run hmmatac test
            • Validate callpeak options
            • Validate HMMATAC
            • Validate predictd options
            • Validate filterdup options
            • This method saves the list of available regions
            • Validate the given options
            • Generate R script to r script
            • Validate Cmbreps options
            • Save predicted probabilities to BED file
            • Load the treatment files
            • Load options from options file
            • Validate BGCMP arguments
            • Validate options
            • Validate function callvar
            • Generate the path to the states of each candidate in the candidate
            • Check for common names in treatment and control files
            • Calculate the maximum number of duplicate tags
            • Save a BED file
            Get all kandi verified functions for this library.

            MACS Key Features

            No Key Features are available at this moment for MACS.

            MACS Examples and Code Snippets

            No Code Snippets are available at this moment for MACS.

            Community Discussions

            QUESTION

            Get lowest mac address
            Asked 2022-Apr-08 at 01:42

            What is the best way to get the network adapter with the lowest mac address? There are multiple network adapters named Intel(R) I210, just need the one with the lowest mac address.

            ...

            ANSWER

            Answered 2022-Apr-08 at 01:42

            You can use Sort-Object to sort the output from Get-NetAdapter based on the .MacAddress property and then get the lowest Mac Address based on that sort.

            Source https://stackoverflow.com/questions/71790321

            QUESTION

            What is the macOS alternative to namespaces(7) in Linux or jails in FreeBSD?
            Asked 2022-Apr-03 at 12:01

            When I was using Linux I used to use Linux namespaces:

            https://man7.org/linux/man-pages/man7/namespaces.7.html

            Also on FreeBSD, there are jails:

            https://www.freebsd.org/cgi/man.cgi?jail

            I was wondering what the alternative was on macOS 12? I'm new to Macs so I'm just trying to learn the system and any features it might have.

            ...

            ANSWER

            Answered 2022-Apr-03 at 12:01

            The equivalent feature to FreeBSD's jails and linux namespaces for macOS is the App Sandbox.

            You can find relevant details in the App Sandbox Design Guide.

            Source https://stackoverflow.com/questions/71723099

            QUESTION

            How do I detect QEMU emulation from within a Docker container?
            Asked 2022-Mar-28 at 07:26

            From within a docker container (in my case running a Debian Busty based image) how can I detect whether it's running under QEMU emulation (as happens on ARM Macs for AMD64 images)?

            From the non-docker perspective I've seen suggestion that cpuinfo might surface this, but it doesn't yield anything directly QEMU related when run from inside my container:

            ...

            ANSWER

            Answered 2022-Mar-28 at 07:26

            There are more ways to detect that the container is running under the emulation, however the most reliable way is to use identify if the entry point is emulated.

            When a container is created, the entry point will become the PID 1. The mechanism that Docker uses for the qemu emulation will detect that the entry point is for a different architecture and will involve the emulator to emulate the architecture. You can read more about the mechanism used in this post.

            Since the entry point will be emulated, the process name will be replaced with the qemu-xxxx where the xxxx is the architecture that will be emulated. We can identify if our entry pint process was substituted for qemu if we call ps -uax as in the following example:

            Source https://stackoverflow.com/questions/70116861

            QUESTION

            Spring Cloud Config Server GitHub SHA-1 error
            Asked 2022-Mar-22 at 03:13
            Context

            This is regarding a Spring Cloud Config Server hobby project (with @EnableConfigServer).

            Yesterday, the application could be started.

            Today, the application failed to start because of a Git communication error.

            From GitHub's official blog post, it is mentioned that SHA-1 is no longer supported starting from 15 March 2022. And that explains the results I'm getting these 2 days.

            March 15, 2022

            Changes made permanent.

            We’ll permanently stop accepting DSA keys. RSA keys uploaded after the cut-off point above will work only with SHA-2 signatures (but again, RSA keys uploaded before this date will continue to work with SHA-1). The deprecated MACs, ciphers, and unencrypted Git protocol will be permanently disabled.

            Even if I didn't delete the existing SSH key, it still failed to start today. But anyway, now the only key under the "Deploy keys" section of the repository settings is an SSH key that was added after the March 15, 2022 cut off date.

            Dependency versions

            Dependency Management:

            Dependency Version spring-cloud-dependencies Hoxton.SR12

            Dependency:

            Dependency Version spring-cloud-config-server (Managed) Spring application configurations

            application.yml:

            ...

            ANSWER

            Answered 2022-Mar-16 at 14:07

            I have a same problem.

            See https://github.com/spring-cloud/spring-cloud-config/issues/2061

            For right now, I have a dirty workaround: use https uri, username and password(maybe personal secret token).

            Source https://stackoverflow.com/questions/71489256

            QUESTION

            Validate Github Webhook HMAC Signature Lucee Coldfusion and CFWheels
            Asked 2022-Mar-10 at 12:09

            I am trying to verify the signature of my webhooks from github. Following their documentation, there is only an example for ruby:

            ...

            ANSWER

            Answered 2022-Mar-10 at 12:09

            I've just created a test Github webhook and was able to successfully verify a push event in Lucee using the following basic code:

            Source https://stackoverflow.com/questions/71414909

            QUESTION

            Pysftp fails with "Authentication failed" and "Server did not send a server-sig-algs list; defaulting to our first preferred algo ('rsa-sha2-512')"
            Asked 2022-Jan-28 at 09:18

            I have ec2 instance with ubuntu v20.04 and it has python v3.8.10 and pysftp 0.2.9.

            I have generate .pem file from .ppk file using below command

            puttygen sftp_server.ppk -O private-openssh -o sftp_server.pem

            I am able to connect successfully to sftp server using command line-

            ...

            ANSWER

            Answered 2022-Jan-28 at 09:18

            The error comes form underlying Paramiko and is discussed here:
            Paramiko authentication fails with "Agreed upon 'rsa-sha2-512' pubkey algorithm" (and "unsupported public key algorithm: rsa-sha2-512" in sshd log)

            Though pysftp does not expose the disabled_algorithms parameter.

            You better switch to using Paramiko directly. The pysftp is abandoned project. See pysftp vs. Paramiko.

            Source https://stackoverflow.com/questions/70812056

            QUESTION

            How to Set Directory Metadata in Azure File Share directory
            Asked 2022-Jan-20 at 16:49

            I am trying to Set the meta deta of a directory in Azure File share using Powershell. Rest API Documentation is https://docs.microsoft.com/en-us/rest/api/storageservices/set-directory-metadata If I remove the x-ms-meta-name:value from below code then it works and it deletes the existing metadata but when I try to add it. it gives an authentication error. Error is mentioned at the end of post. Below is the script

            ...

            ANSWER

            Answered 2022-Jan-20 at 16:49

            Please change the following line of code:

            Source https://stackoverflow.com/questions/70788764

            QUESTION

            Nim 1.4 Compile - Modify default compile flags on MacOS - issue with clang ld: library not found for -lrt
            Asked 2022-Jan-15 at 14:42

            For some reason on my Mac when I am using nim 1.4 with clang it always builds with the -lrt compile flag which breaks since that's not on Macs.

            So every time I need to do nim c --listCmd [my nim file].nim, get the compile command and delete the -lrt before running again, which works fine.

            There must be some setting that's making nim or nimble always include -lrt in the compile flags but I don't know how to go about troubleshooting this.

            I'm stuck on 1.4 due to some {.requiresInit.} issues that break in 1.6.

            MacOS 12.1 - ARM Nim 1.4

            ...

            ANSWER

            Answered 2022-Jan-15 at 14:42

            Thanks to hola for finding out that one of my dependencies always passes -lrt, https://github.com/dfdeshom/nimrdkafka/blob/6d18bed51922fc44f3565566b67e35b37dc5ce70/nimrdkafka.nim#L48

            Solution would have to be to modify that import.

            Source https://stackoverflow.com/questions/70680615

            QUESTION

            Paramiko authentication fails with "Agreed upon 'rsa-sha2-512' pubkey algorithm" (and "unsupported public key algorithm: rsa-sha2-512" in sshd log)
            Asked 2022-Jan-13 at 14:49

            I have a Python 3 application running on CentOS Linux 7.7 executing SSH commands against remote hosts. It works properly but today I encountered an odd error executing a command against a "new" remote server (server based on RHEL 6.10):

            encountered RSA key, expected OPENSSH key

            Executing the same command from the system shell (using the same private key of course) works perfectly fine.

            On the remote server I discovered in /var/log/secure that when SSH connection and commands are issued from the source server with Python (using Paramiko) sshd complains about unsupported public key algorithm:

            userauth_pubkey: unsupported public key algorithm: rsa-sha2-512

            Note that target servers with higher RHEL/CentOS like 7.x don't encounter the issue.

            It seems like Paramiko picks/offers the wrong algorithm when negotiating with the remote server when on the contrary SSH shell performs the negotiation properly in the context of this "old" target server. How to get the Python program to work as expected?

            Python code

            ...

            ANSWER

            Answered 2022-Jan-13 at 14:49

            Imo, it's a bug in Paramiko. It does not handle correctly absence of server-sig-algs extension on the server side.

            Try disabling rsa-sha2-* on Paramiko side altogether:

            Source https://stackoverflow.com/questions/70565357

            QUESTION

            How does this video on C avoid *Error: Variable-sized object may not be initialized* during compilation?
            Asked 2022-Jan-03 at 23:29

            *** EDIT - I know it is a long post and I know I have used some 'interesting' language choices. And, I'm choosing to believe the three answers I've had so far were made with good intent - for that I thank you. But, I really must insist, if you are not willing to read the whole post thoroughly or if you don't understand what it is I am actually asking, please save both our time and refrain from posting. ***

            I have been searching for an answer to exactly the same question posed here - same online course, same lecturer; I recognise the code from the video.

            I quickly found solutions in the form of #define and using an enum, but that still didn't really solve how the lecturer got his code to compile; and, I would like to actually comprehend, not just make it work so, I tried to dig deeper.

            The professor in question doesn't ever actually show the code compilation, it's always a "here's one I compiled earlier" scenario - so I had included the possibility the error was in that unseen stage as indicated by the two answers on the page: he may well have been using g++ or clang.

            However, my search was most circuitous, leading me hither and tither across the net, and in my quest, before I came across the above linked answers and amongst other things I came across this video where at around the 9 minute mark he compiles this code:

            ...

            ANSWER

            Answered 2022-Jan-03 at 23:29

            This is a result of constant folding in the clang compiler.

            The instructor is compiling the program on a Mac, and on that platform "gcc" is an alias for "clang". While gcc does not perform this folding for a VLA, clang does.

            From the clang documentation (version 10):

            Differences between all c* and gnu* modes:

            • c* modes define __STRICT_ANSI__.
            • Target-specific defines not prefixed by underscores, like “linux”, are defined in gnu* modes.
            • Trigraphs default to being off in gnu* modes; they can be enabled by the -trigraphs option.
            • The parser recognizes asm and typeof as keywords in gnu* modes; the variants __asm__ and __typeof__ are recognized in all modes.
            • The Apple “blocks” extension is recognized by default in gnu* modes on some platforms; it can be enabled in any mode with the -fblocks option.
            • Arrays that are VLA’s according to the standard, but which can be constant folded by the frontend are treated as fixed size arrays. This occurs for things like int X[(1, 2)];, which is technically a VLA. c * modes are strictly compliant and treat these as VLAs.

            Source https://stackoverflow.com/questions/70572040

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

            Vulnerabilities

            No vulnerabilities reported

            Install MACS

            The common way to install MACS is through PYPI) or conda. Please check the INSTALL document for detail.
            x86_64
            aarch64
            armv7
            ppc64le
            s390x

            Support

            Please read our CODE OF CONDUCT and How to contribute documents. If you have any questions, suggestion/ideas, or just want to have conversions with developers and other users in the community, we recommand you use the MACS Discussions instead of posting to our Issues page.
            Find more information at:

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