proActiv | Estimation of Promoter Activity from RNA-Seq data | Genomics library
kandi X-RAY | proActiv Summary
kandi X-RAY | proActiv Summary
proActiv is an R package that estimates promoter activity from RNA-Seq data. proActiv uses aligned reads and genome annotations as input, and provides absolute and relative promoter activity as output. The package can be used to identify active promoters and alternative promoters. Details of the method are described in Demircioglu et al. HTML documentation of proActiv, including a complete step-by-step workflow and a function manual, is available at Additional data on differential promoters in tissues and cancers from TCGA, ICGC, GTEx, and PCAWG is available at
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proActiv Key Features
proActiv Examples and Code Snippets
library(proActiv)
## List of STAR junction files as input
files <- list.files(system.file('extdata/vignette/junctions',
package = 'proActiv'), full.names = TRUE)
## Vector describing experimental condition
conditi
## From GTF file path
gtf.file <- system.file('extdata/vignette/annotation/gencode.v34.annotation.subset.gtf.gz',
package = 'proActiv')
promoterAnnotation.gencode.v34.subset <- preparePromoterAnnotation(file = gtf.file,
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("proActiv")
Community Discussions
Trending Discussions on proActiv
QUESTION
I started using the repeatable jobs in bull and everything seems to be working well for me. However, I noticed that each iteration leaves a job in Redis:
- "test:foo:repeat:7a140b0cf5b3ee29cb164b7c9cc03bc3:1619132310000"
- "test:foo:repeat:7a140b0cf5b3ee29cb164b7c9cc03bc3:1619132280000"
- "test:foo:repeat:7a140b0cf5b3ee29cb164b7c9cc03bc3:1619132360000"
and the list keeps growing. I tried to do a job.remove() within the process function, but it threw an error... can't remove repeatable jobs I guess. I'm assuming these will eventually be cleaned up by Redis, but is there something more proactive I can do to keep Redis clean?
...ANSWER
Answered 2021-Apr-29 at 21:10Needed to add the 'removeOnComplete' value to the jobOptions.
QUESTION
I have javascript to fetch json information. I will be storing this json file locally (I downloaded an example file and added birthdate object for my use example from https://jsonplaceholder.typicode.com/users)
I am trying to parse the returned JSON information and post the contents into 2 seperate div's. I have a json object named "birthdate". In my script, I have a var set to call today's date named "today". It prints the date as "05-12" in console, and that is how I have the "birthdate" formatted in JSON as well. I don't need the year or time.
What I would like is to have the script compare "today" with the json object "birthdate". If today = birthdate, then I would like to have that entry information displayed in the user-list-today div to appear under the Birthday Today section of the page.
If today does not equal birthdate, I would like to have all other entries displayed in the user-list-future div to appear under the Birthday Future section of the page.
Nothing should be posted in both areas, only one or the other.
Any help that anyone could provide would be greatly appreciated. I will include all of my code below. The snippet may give error because I have local path to JSON file instead of online version.
Here is my codepen of it codepen doesnt have the birthday JSON object https://codepen.io/abc-123-webguy/pen/poegaLq
...ANSWER
Answered 2021-May-12 at 21:47This is because you are appending the same node to two different divs. If you look at the documentation to appendChild
here, you can see this:
QUESTION
With YouTube Data API we can parse comments from a certain video, reply to these comments, modify and delete our comments etc. But in this aforementioned documentation I didn't find the way to fetch the user comments in real-time. So the situation is like - apart from fetching comments when the API is called, I want the API to proactively update me with most recent changes if any new comment arrives or any modification or deletion happens. Any way to achieve this?
...ANSWER
Answered 2021-Apr-26 at 07:18The only way to find out of there have been comments its to poll the API and check every now and then. There are no push notifications for comments if that's what you are looking for.
Push notifications only work for.
- uploads a video
- updates a video's title
- updates a video's description
QUESTION
I have a problem sending proactive messages using the Bot Framework with Python. First what I need is to get the message body from Outlook, and then the bot must send that as a message to all the chats where it was added.
To do that, first I created a new file and called it Email.py.
To read every incoming message body I simply used while true:
and time.sleep()
Here is my code example:
...ANSWER
Answered 2021-Apr-11 at 12:41As we have discussed some logic has to change
- Move your code out of the on_members_added_activity function
- Use Proactive concept to send the message
-Vinoth
QUESTION
As a part of a use case, I want to send user a proactive message from bot. I am following this document related to sending proactive messages to bot.(Send Proactive message)
I am trying to send proactive message to the user when the user has not interacted with bot previously. For this scenario, I need to call 'Install App for Users' graph API and cache the necessary values from the conversation Update event bot receives upon installation.(Send proactive message when user has not interacted with bot)
However, the permissions required to call this API are marked in private preview mode on the permissions reference page. (Permission Reference) I want to know if there is any other way to send proactive message to bot other than the way mentioned above. I am attaching the screenshot of documentation for reference.
...ANSWER
Answered 2021-Mar-24 at 12:52From the Teams App Install permissions reference, installing an application for the user can also use this permission: TeamsAppInstallation.ReadWriteForUser
. Although this is more privileged permission and requires admin consent, this is what should be used given that TeamsAppInstallation.ReadWriteSelfForUser
is in private preview.
QUESTION
The organization that I work for previously used Slack as our collaboration tool. With Slack, I was able to register an app in the workspace and use the provided access tokens to invoke the API to send a message to a user from our external web application. It was very straightforward. There was no intermediate app that needed to be coded to enable this messaging.
Recently, we've transitioned from Slack to MS Teams, and in looking over the Graph API documentation, there does not currently appear to be a way to proactively send a message from an external application to a user. The available permissions for the chatMessage endpoint indicate the availability of only a delegated permission to send a message on behalf of a specific user; no permission exists to send a message on behalf of an external application.
Is it possible to use the Graph API to directly send a message from an external application to a user? Or must a bot application be created in order to achieve this?
...ANSWER
Answered 2021-Apr-01 at 02:29It must be a bot application to achieve above mentioned requirement. ChatMessage endpoint works to send a message on behalf of user only.
QUESTION
I am building a custom app for MS Teams that sends Proactive chat messages to the users of each of the teams. When I give the app to the teams admin, they will publish the app, but I am not sure how the admin will install for their users, so that I receive conversation_id of all the users in their teams after it has been installed. I am aware that it is possible through Graph API and is looking to eliminate the app installation through Graph Api.
...ANSWER
Answered 2021-Mar-23 at 19:23It's possible for an admin to do this using the Teams Admin section in the Microsoft 365 Tenant Admin screens. Specifically, you're wanting to set up something called "App Setup Policies". See here for more: https://docs.microsoft.com/en-us/microsoftteams/teams-app-setup-policies#create-a-custom-app-setup-policy
Using these policies, admins can pre-install the app, and can even pin it on the left menu. They can also choose to do this for all users, or just a specified group.
To be clear though, this will install the app to the users in a -personal- context - it will NOT install the app to any -actual- Teams / Channels or Group Chats - you'd need to use Graph for that, and even then it will only be able to install to -existing- Channels or Chats and won't automatically cover new ones added after that, if that's what you were trying to achieve.
QUESTION
I would like to save the conversation references to a blob file or SQL DB so that I can download this file and retrieve the conversation references and then send proactive messages to the users. I know that there is a sample that allows me to save the conversation references in a dictionary, but obviously this dictionary is deleted after a deployment of a new version of the bot and so I can't message the users anymore. So I thought to save this dictionary in a blob file in order to recover it and not to lose the conversation references. But this practice doesn't work.
I do the following to save the dictionary.
...ANSWER
Answered 2021-Mar-15 at 22:14I'm not sure why this was removed from the docs, but you always need to trust the service URL in order to send proactive messages in Teams, as explained in this answer: Proactive message not working in MS Teams after bot is restarted
EDIT: This is apparently no longer true for all languages, so you may not have to do it in Python for much longer
QUESTION
I can't seem to figure out how to proactively message a MS teams channel using a Python Bot (botframework).
- An user installs my third-party MS teams bot, adding it to one of their Teams channels.
- My Bot needs to send ad-hoc messages as part of an event from an unrelated back-end system.
The botframework does not let you message channels at will, it needs a conversation reference. You can get a conversation reference in various ways, such as someone messaging the bot, or fetching the list of channels and constructing a conversationId
from that.
The documentation will have you believe that it is in fact possible to send message at will, using the following steps:
- Get the user ID or team/channel ID (if needed).
- Create the conversation or conversation thread (if needed).
- Get the conversation ID.
- Send the message.
For step 1, how/when do I get the channel ID if there are no events that my Bot has been added to a channel?
For step 2, how do I create a conversation if I don't know what team channels there are?
ConclusionDoes someone know how to send a message to a MS Teams channel using a Python app/bot? It should not require user interaction. The app/bot gets added to a Teams channel, and it should immediately post a message inside this channel.
...ANSWER
Answered 2021-Jan-13 at 16:30I'm working on a sample for the pnp Teams samples repo on GitHub that I'm hoping to submit in the next few days. I haven't started on the documentation yet, but the code is fully functional, with both a C# and a Node.js version of the backend, which sends a -very- simple proactive message example (showing the most basic things you need) - hopefully it can be of use even though it's not in Python - see https://github.com/HiltonGiesenow/teams-dev-samples/tree/add-proactive-messaging-sample/samples/bot-proactive-messaging/src
QUESTION
In my 1 node AKS, I deploy multiple job resources (kind:jobs) that are terminated after the task is completed. I have enabled Cluster Autoscaler to add a second node when too many jobs are consuming the first node memory, however it scales out after a job/pod is unable to be created due to lack of memory.
In my job yaml I also defined the resource memory limit and request.
Is there a possibility to configure the Cluster Autoscaler to scale out proactively when it reaches a certain memory threshold (e.g., 70% of the node memory) not just when it cannot deploy a job/pod?
...ANSWER
Answered 2021-Mar-10 at 11:49In Kubernetes you can find 3 Autoscaling Mechanisms: Horizontal Pod Autoscaler, Vertical Pod Autoscaler which both can be controlled by metrics usage and Cluster Autoscaler.
As per Cluster Autoscaler Documentation:
Cluster Autoscaler is a tool that automatically adjusts the size of the Kubernetes cluster when one of the following conditions is true:
- there are pods that failed to run in the cluster due to insufficient resources.
- there are nodes in the cluster that have been underutilized for an extended period of time and their pods can be placed on other existing nodes.
In AKS Cluster Autoscaler Documentation you can find note that CA
is Kubernetes Component, not something AKS specific:
The cluster autoscaler is a Kubernetes component. Although the AKS cluster uses a virtual machine scale set for the nodes, don't manually enable or edit settings for scale set autoscale in the Azure portal or using the Azure CLI. Let the Kubernetes cluster autoscaler manage the required scale settings.
In Azure Documentation - About the cluster autoscaler you have information that AKS clusters can scale in one of two ways:
The
cluster autoscaler
watches for pods that can't be scheduled on nodes because of resource constraints. The cluster then automatically increases the number of nodes.The
horizontal pod autoscaler
uses the Metrics Server in a Kubernetes cluster to monitor the resource demand of pods. If an application needs more resources, the number of pods is automatically increased to meet the demand.
On AKS
you can adjust a bit your Autoscaler Profile
to change some default values. More detail can be found in Using the autoscaler profile
I would suggest you to read the Understanding Kubernetes Cluster Autoscaling article which explains how CA
works. Under Limitations
part you have information:
ConclusionThe cluster autoscaler doesn’t take into account actual CPU/GPU/Memory usage, just resource requests and limits. Most teams overprovision at the pod level, so in practice we see aggressive upscaling and conservative downscaling.
Cluster Autoscaler
doesn't consider actual resources usage. CA
downscale or upscale might take a few minutes depending on cloud provider.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install proActiv
proActiv estimates promoter activity from RNA-Seq data. Promoter activity is defined as the total amount of transcription initiated at each promoter. proActiv takes as input either BAM files or junction files (TopHat2 or STAR), and a promoter annotation object of the relevant genome. An optional argument condition can be supplied, describing the experimental condition corresponding to each input file. Here we demonstrate proActiv with STAR junction files (Human genome GRCh38 GENCODE v34) as input. These files are taken from the SGNEx project but restricted to the chr1:10,000,000-30,000,000 region, and can be found at extdata/vignette:.
extdata/vignette/SGNEx_A549_Illumina_replicate1-run1.subset.SJ.out.tab.gz
extdata/vignette/SGNEx_A549_Illumina_replicate3-run1.subset.SJ.out.tab.gz
extdata/vignette/SGNEx_A549_Illumina_replicate5-run1.subset.SJ.out.tab.gz
extdata/vignette/SGNEx_HepG2_Illumina_replicate2-run1.subset.SJ.out.tab.gz
extdata/vignette/SGNEx_HepG2_Illumina_replicate4-run1.subset.SJ.out.tab.gz
extdata/vignette/SGNEx_HepG2_Illumina_replicate5-run1.subset.SJ.out.tab.gz
assays(results) returns raw/normalized promoter counts, absolute/relative promoter activity and gene expression data
rowData(results) returns promoter metadata and summarized absolute promoter activity by conditions
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