sleuth | Differential analysis of RNA-Seq | Genomics library

 by   pachterlab R Version: v0.30.1 License: GPL-3.0

kandi X-RAY | sleuth Summary

kandi X-RAY | sleuth Summary

sleuth is a R library typically used in Artificial Intelligence, Genomics applications. sleuth has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

sleuth is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via kallisto for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and supports interactive exploratory data analysis via sleuth live. The sleuth methods are described in. H Pimentel, NL Bray, S Puente, P Melsted and Lior Pachter, Differential analysis of RNA-seq incorporating quantification uncertainty, Nature Methods (2017), advanced access.
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              sleuth has a low active ecosystem.
              It has 278 star(s) with 93 fork(s). There are 40 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 92 open issues and 105 have been closed. On average issues are closed in 113 days. There are 5 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of sleuth is v0.30.1

            kandi-Quality Quality

              sleuth has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              sleuth is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              sleuth releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

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            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of sleuth
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            sleuth Key Features

            No Key Features are available at this moment for sleuth.

            sleuth Examples and Code Snippets

            Launch the Sleuth web application .
            javadot img1Lines of Code : 3dot img1License : Permissive (MIT License)
            copy iconCopy
            public static void main(String[] args) {
                    SpringApplication.run(SleuthWebApp.class, args);
                }  

            Community Discussions

            QUESTION

            spring-cloud-starter-sleuth + axon-tracing-spring-boot-starter =?
            Asked 2021-Jun-03 at 15:25

            The title says it all. Is it possible to get spring-cloud-starter-sleuth working together with axon-tracing-spring-boot-starter?

            current log output:

            ...

            ANSWER

            Answered 2021-Jun-03 at 15:25

            It seems axon-tracing-spring-boot-starter is using OpenTracing. OpenTracing is a tracing library that was abandoned and it has never reached a GA/stable release. So even if there would be an easy way, I would not use OpenTracing in production, I would try to move away from it.

            From version 3.0, Spring Cloud Sleuth has abstracted the tracer away and it supports multiple tracer implementations. By default it supports Brave which is a mature tracing library but Sleuth has support for OpenTelemetry as well (Sleuth-OTel). The OpenTelemetry support is incubating and it is not recommended to use in prod since OpenTelemetry Tracing is not entirely stable/GA yet for Java.

            With this, your options are:

            1. Add support to Axon for Brave
              This is what I would recommend, I would start with opening an issue for them
            2. OpenTelemetry theoretically compatible with OpenTracing (check the OpenTelemetry docs)
              You might be able to use Sleuth-OTel and OpenTracing The problem with this is: OpenTracing is abandoned and never went GA, OpenTelemetry Java Tracing is not stable yet, Sleuth-OTel is not stable yet
            3. You can implement OpenTracing support for Sleuth
              I think this is a bad idea, it is a lot of work and OpenTracing is abandoned and never went GA

            Source https://stackoverflow.com/questions/67805955

            QUESTION

            Using Feign builder requests doesn't send trace-id, span-id to child clients but using rest template is showing all headers on child clients
            Asked 2021-May-28 at 06:05

            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 08:16

            The 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.

            Source https://stackoverflow.com/questions/66167917

            QUESTION

            Spring Cloud sleuth memory leak issue
            Asked 2021-May-25 at 19:25

            I am facing issue with spring cloud sleuth as it is leaking memory as I have gone through the dumps of my applications:

            What does 13.05mb (40.3%) of Java Static org.springframework.cloud.sleuth.instrument.async.SleuthContextListener.CACHE

            Spring Cloud Version: Hoxton.SR8 Spring Boot Version: 2.3.3.RELEASE

            Please find the heapdump report below:

            https://heaphero.io/my-heap-report.jsp?p=YXJjaGl2ZWQvMjAyMS8wNS8yNS8tLWhlYXBkdW1wLTE2MjE5MjE0MzYyNTMuaHByb2YtNS00Ni0xLmpzb24=

            pls find the code repo below, which I am using in my appplication, Also on first run there is no memory leakage issue but on successive runs it shows the memory leakage issue as mentioned in the heapdump report

            ...

            ANSWER

            Answered 2021-May-25 at 19:25

            You have a complete mix of versions. Why do you say that you're using Hoxton and Boot 2.3 if you're not using Hoxton, you're using Greenwich and Boot 2.1

            Source https://stackoverflow.com/questions/67671805

            QUESTION

            Jhipster Spring Boot 2 instances of a microservice on different databases
            Asked 2021-May-25 at 19:18

            In my project I'm using Jhipster Spring Boot and I would like to start 2 instances of one microservise at the same time, but on different instances of a database (MongoDB).

            In this microservice I have classes, services, rests that are used for collections A, B C,.. for which now I would like to have also history collections A_history, B_history, C_history (that are structured exactly the same like A, B, C) stored in separated instance of a database. It makes no sense to me to create "really separated" microservice since I would have to copy all logic from the first one and end up with doubled code that is very hard to maintain. So, the idea is to have 2 instances of the same microservice, one for A, B, C collections stored in "MicroserviceDB" and second for A_history, B_history, C_history collections stored in "HistoryDB".

            I've tried with creating 2 profiles, but when I start from a command line History microservice, it is started ok, but if I also try to start "original" microservice at the same time, it is started but immediately history service becomes "original" microservice. Like they cannot work at the same time.

            Is this concept even possible in microservice architecture? Does anyone have an idea how to make this to work, or have some other solution for my problem?

            Thanks.

            application.yml

            ...

            ANSWER

            Answered 2021-May-20 at 09:18

            In general, this concept should be easily achievable with microservices and a suiting configuration. And yes, you should be able to use profiles to define different database connections so that you can have multiple instances running.

            I assume you are overwriting temporary build artifacts, that's why it is not working somehow. But that is hard to diagnose from distance. You might consider using Docker containers with a suiting configuration to increase isolation in this regard.

            Source https://stackoverflow.com/questions/67616962

            QUESTION

            Issues with Upgrading Spring boot from 2.2.2.Release to 2.4.2 Rlease
            Asked 2021-May-20 at 14:32

            We have an existing application which is working fine with the SpringBoot 2.2.2.RELEASE. Now we tried to upgrade it to the SpringBoot 2.4.2 version and application is not getting started and throws the following error. In the classpath I could see only one spring-webmvc-5.3.2.jar file.

            Below is the pom.xml for the referance:

            ...

            ANSWER

            Answered 2021-Jan-29 at 14:01

            QUESTION

            Integration of Spring Cloud Gateway With Spring Cloud Sleuth
            Asked 2021-May-14 at 10:54

            I could not find any example which is integrating Spring cloud Sleuth with the Spring Cloud Gateway. Want a Sample Project doing the Integration successfully.

            ...

            ANSWER

            Answered 2021-May-14 at 10:54

            If you use your favorite search engine and type in spring cloud sleuth gateway sample most likely one of the first results will be this https://github.com/spring-cloud-samples/spring-cloud-sleuth-samples/tree/main/gateway

            Source https://stackoverflow.com/questions/67532866

            QUESTION

            How do I access the current span and trace ids in a Spring Reactor context?
            Asked 2021-May-11 at 17:44

            In my Spring Boot WebFlux application, I am using Reactor. I have set spring.sleuth.reactor.instrumentation-type=manual and am using @ContinueSpan on a service method. I see from the code that the span is created, started and ended appropriately in a reactive way.

            Later, in the Flux I need to extract the trace information.

            The code I am using injects Tracer and I use Tracer.currentSpan().context() to try to get to the trace context. I can successfully get the currentSpan() until I hit a call to an R2DBC repository method, after which the currentSpan is null. I can make the span "current" by annotating the repository method, but I do not want to do that unless it's necessary. I'd like to understand the underlying "problem".

            I have also looked at CurrentTraceContext in the Reactor Subscription Context and see that it answers as Tracer does. Supporting both seems to be a threadlocal-ly supported trace context.

            Oddly, if I look at TraceContext in the Subscriber context, the trace, parent, and span ids are there. It appears that WebFluxSleuthOperators.currentTraceContext(Context...) does this - so I have to believe that this is the appropriate vehicle for obtaining the trace context.

            So, a few questions:

            1. Is WebFluxSleuthOperators.currentTraceContext(Context...) [TraceContext in the Reactor Subscription context] the proper way to get the up-to-date trace context?

            2. Looking at ReactorSleuthMethodInvocationProcessor, a reference to the current span and trace context are given to the SpanSubscriber which puts them in the Subscriber context. As mentioned earlier, subscribe() and next() are invoked within the context of that span. Why would a method such as a call to a r2dbc repository method effectively "erase" the tracer.currentSpan() but leave the trace context alone?

            I'd love to understand this a bit more deeply and will look at the source more. But any insight right now is greatly appreciated. Thank you very much in advance.

            ...

            ANSWER

            Answered 2021-May-11 at 17:44

            To access the current span in a Reactor flow in Spring, use the Span or TraceContext found in the Subscriber Context.

            Mono.deferContextual(contextView -> Mono.just(contextView.get(TraceContext.class)))

            Or, better yet, use WebFluxSleuthOperators.currentTraceContext(Context.of(contextView)))

            Accessing the span through the Tracer bean may not produce the current span - as the current thread may be different than the one that originated the span and brought it into scope. This was confirmed through debugging.

            Source https://stackoverflow.com/questions/67443034

            QUESTION

            Configuring spring cloud sleuth and logback to log baggage fields
            Asked 2021-May-05 at 17:20

            Following the spring cloud sleuth documentation, I've configured an app properties with the following:

            ...

            ANSWER

            Answered 2021-May-05 at 17:20

            I've made a novice mistake and only needed to define the CONSOLE_LOG_PATTERN before including the defaults and other appenders.

            Source https://stackoverflow.com/questions/67405815

            QUESTION

            my list of users or anything else wont apear unless I add a new user
            Asked 2021-May-05 at 12:39

            I can't access to my usersList: if I don't add a user first I can't user neither of the other paths of my controller. here, I can't get my users list unless I add a user first and I am using postgres DB then if I add a user everything else works and it brings me all the users in the database the error that I got

            controller

            ...

            ANSWER

            Answered 2021-May-05 at 12:39

            Your modelMapper isn't initialized when you call mapToDto at first. This only happens in mapToEntity Method.

            Source https://stackoverflow.com/questions/67399242

            QUESTION

            How do you profile a Go fasthttp/router application?
            Asked 2021-Apr-29 at 17:01

            I'd like to profile my Go HTTP server application to see if there are places where it can be optimized. I'm using the fasthttp package with the fasthttp/router package, and I'm struggling to figure out how to hook up pprof.

            The basic setup looks like this, obviously very abridged:

            ...

            ANSWER

            Answered 2021-Apr-29 at 17:01

            You can use net/http/pprof for profiling.
            fasthttp provides custom implementation for the same. You can use that same as the net/http/pprof.

            To use this, register the handler as:

            Source https://stackoverflow.com/questions/67320764

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

            Vulnerabilities

            No vulnerabilities reported

            Install sleuth

            The easiest way to install is using the devtools package through Bioconductor.
            If you have conda, a cross-platform package manager installed, you can install sleuth via the bioconda channel.

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