rgr | Researcher Gene Registry. Originally developed | Genomics library

by PavlidisLab Java Version: v1.4.9 License: Apache-2.0

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | rgr Summary

rgr is a Java library typically used in Artificial Intelligence, Genomics applications. rgr has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Researcher Gene Registry. Originally developed for the Canadian Rare Disease Models & Mechanisms Network

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Security

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Support

rgr has a low active ecosystem.

It has 5 star(s) with 2 fork(s). There are 4 watchers for this library.

It had no major release in the last 12 months.

There are 67 open issues and 78 have been closed. On average issues are closed in 43 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of rgr is v1.4.9

Quality

rgr has no bugs reported.

Security

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

License

rgr is licensed under the Apache-2.0 License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

rgr releases are available to install and integrate.

Build file is available. You can build the component from source.

Top functions reviewed by kandi - BETA

kandi has reviewed rgr and discovered the below as its top functions. This is intended to give you an instant insight into rgr implemented functionality, and help decide if they suit your requirements.

Updates the user s profile and publications
Converts an OrganInfo to a UserOrgan
Create a contact email token
Search users by a given gene id
Obtain a summary of available ontologies from the remote resources
Collects all futures into a map
Updates the ontology terms
Saves a term by ID
Updates gene orthologs
Parses the given input stream into records
Display the change password
Creates new service account
Search users by description
The strategy for the flyway
Updates the cached data
Sends a support form to the user
Loads an organology from the system
Search for users
Updates the reactome pathways in the given ontology
Writes an OBO format to the given writer
Updates the genes file
Search users by name
Updates the terms and traits for a given taxon
Returns a list of users by a specific name and description
Start the downloader
Registers a new user

Get all kandi verified functions for this library.

rgr Key Features

No Key Features are available at this moment for rgr.

rgr Examples and Code Snippets

No Code Snippets are available at this moment for rgr.

Community Discussions

Trending Discussions on rgr

Remove items from Object using their Index using Lodash

How would I plot my linear regression model with a line of best fit?

Postgresql how handle json array with select query to attribute wise in table?

Something wrong with my checkpoint file when using torch.load()

Difference between gridCV.score method on training data vs gridCV.best_score_

Merge two layers with different shape reproducing SiamRPN

Apache Scala/Python Spark 2.4.4: Group data by year range to generate/analyze new feature

Find & Replace text within an xml file

How can I count the number of days that match between a data frame with two vectors (start date and end date) and a vector of dates?

How to remove sub-strings from list lines that start with a certain character sequence and generate an output file

QUESTION

Remove items from Object using their Index using Lodash

Asked 2021-Mar-12 at 11:03

I have an object like this:

...

ANSWER

Answered 2021-Mar-12 at 11:03

I managed to fix it using the following code:

Source https://stackoverflow.com/questions/66569536

QUESTION

How would I plot my linear regression model with a line of best fit?

Asked 2020-Dec-03 at 12:25

I have just trained a linear regression model, getting my intercept and coefficient for house prices based on the "number_rooms" and "price". But I am just a bit unsure on how to plot my regression model using a scatter plot with a line of best fit.

Any help would be much appreciated on how to do this - thanks!

Here's my code:

...

ANSWER

Answered 2020-Dec-03 at 12:08

That's quite simple, try this once-

Source https://stackoverflow.com/questions/65125108

QUESTION

Postgresql how handle json array with select query to attribute wise in table?

Asked 2020-Aug-26 at 14:32

[
  {
    "passengerId": "RGR",
    "passengerFirstName": "",
    "passengerLastName": "",
    "passengerPaxType": "",
    "passengerBasicFare": 0,
    "passengerTotalTax": 0,
    "passengerTransactionAmount": 0,
    "otherCharges": [
      {
        "passengerId": "RGR",
        "chargeCodeAndType": "",
        "chargeAmount": 0,
        "passengerid": 0
      }
    ]
  },
  {
    "passengerId": "Test",
    "passengerFirstName": "",
    "passengerLastName": "",
    "passengerPaxType": "",
    "passengerBasicFare": 0,
    "passengerTotalTax": 0,
    "passengerTransactionAmount": 0,
    "otherCharges": [
      {
        "passengerId": "Test",
        "chargeCodeAndType": "",
        "chargeAmount": 0,
        "passengerid": 0
      }
    ]
  }
]

...

ANSWER

Answered 2020-Aug-26 at 14:32

I still don't understand what exactly the output is you want.

But maybe something like this?

Source https://stackoverflow.com/questions/63597958

QUESTION

Something wrong with my checkpoint file when using torch.load()

Asked 2020-Aug-15 at 13:53

When I use torch.load to load one checkpoint:

...

ANSWER

Answered 2020-Aug-15 at 13:53

I have found the solution. Because I'm using different clusters to train and debug, torch version of each is different. When saving the model, the torch version is 1.6.0 and it's 1.1.0 when loading it.

Source https://stackoverflow.com/questions/63406621

QUESTION

Difference between gridCV.score method on training data vs gridCV.best_score_

Asked 2020-May-03 at 10:07

I have a question about the difference between a randomsearch.score method (score 1) and randomsearch.best_score_ attribute (score 2).

Particularly when randomsearch.score is applied to X_train and y_train.

I thought the randomsearchCV automatically looks for the params that give the highest score on the training set? I would have assumed the randomsearch.score(Xtrain, ytrain) would be the same as the randomsearch.best_params_ score?

...

ANSWER

Answered 2020-May-03 at 10:07

With random_search.score(X_train, y_train), you are testing on same data you've used for training, hence such a high score. This is a (almost) completely meaningless information**, as it doesn't tell you how well your model will perform in unseen data.

cv=5 means your data was partitioned 5 times for each hyper-parameter setting, with 20% data used for testing, and 80% used for training in each partition. Result of these 5 test set is then averaged. The highest such average among all possible hyper-parameter setting is then recorded in random_search.best_score_. So the crucial difference is you aren't evaluating performance on same data used for training, hence comparably lower score.

random_search.score(X_test, y_test) is same as best_score_ in that you are evaluating model on unseen data, but it is better indicator of actual generalization performance. Unlike score 2 however, your model has been trained with 100% training data (as opposed to 80%). This is one possible explanation as to why score 3 is better than score 2.

**If this value is low, you know your model is underfitting, and should try increasing model complexity, like adding more hidden layers to NN, or increasing max_depth of decision tree.

Source https://stackoverflow.com/questions/58706798

QUESTION

Merge two layers with different shape reproducing SiamRPN

Asked 2019-Dec-16 at 09:08

I'm trying to reproduce this paper SiameseRPN using Keras. The architecture is presented as below.

its give this in my code.

...

ANSWER

Answered 2019-Dec-16 at 09:08

Yes, Keras.layers.concatenate requires both the Convolutional Layers passed to it to have the same shape.

In this case, you can use UpSampling Layer.

For Example, suppose the Shape of cls_x is (None, 80, 128, 8) and the Shape of cls_z is (None, 40, 64, 8), you can use

Source https://stackoverflow.com/questions/55140297

QUESTION

Apache Scala/Python Spark 2.4.4: Group data by year range to generate/analyze new feature

Asked 2019-Nov-18 at 21:41

I've following data frame which I generated for feature engineering and now in order to drive another feature, I am trying to create purchaseYearRange column where I want to create a column with 3 year range and aggregate modelRatio, purchaseRatio values by itemNo, modelnumber and valueClass columns.

E.g.: For itemNo#7010032, we will have a row with 1995-1996-1997 value in new purchaseYearRange column and modelRatio, purchaseRatio values for these years will be summed up in the respective row. Next, I'll do that same for next 3 years which will be 1996-1997-1998, 1997-1998-1999, etc.

Also, this item has one row with itemClass - RGR, for that row we'll only have that row with 1996 data.

Basically, check for 3 years data in dataframe and if it exists then sum modelRatio, purchaseRatio for three-year range window. If three-year data doesn't exist then sum for two or one year based on data availability.

DataFrame

...

ANSWER

Answered 2019-Nov-18 at 21:41

IIUC, you can use Spark SQL Window function as following: (make sure the purchaseYear is a numeric or timestamp column)

Edit: per comments, added all_puchase_years to include 3-year sequence. Notice that ORDER BY itemNo, purchaseYear clause is only for demonstration purpose.

Source https://stackoverflow.com/questions/58920120

QUESTION

Find & Replace text within an xml file

Asked 2019-May-31 at 09:28

I am trying to create a batch-file which will install an agent in a silent manner. Once the agent has installed I will need to navigate into the agent directory and edit a file called agent.xml.

The agent.xml file looks like the below:

...

ANSWER

Answered 2019-May-31 at 09:28

First of all, this link has numerous methods of doing this flexibly.

If you want a quick method, assuming that what you want to replace will always be in the form of , and there's no ! in your file, you can use this:

Source https://stackoverflow.com/questions/56391613

QUESTION

How can I count the number of days that match between a data frame with two vectors (start date and end date) and a vector of dates?

Asked 2019-May-26 at 16:28

I have a very large data set (>12,000 rows) that contains two vectors of the start and end date of a measurement (relative growth rate). Each row has an individual, the date of the initial measurement, the date of the final measurement, and then the growth rate associated with that window. I want to count the number of days within each growth measurement that match dates that are in a separate vector. So ideally I would be adding a vector to the data frame that gives me a count of the number of matching days between the dates in the df and the external vector for each individual's growth rate.

Sample of what the data frame looks like, but in actuality it is much, much larger

...

ANSWER

Answered 2019-May-26 at 14:29

You could convert DaysToMatch to date and call countDays function using mapply

Source https://stackoverflow.com/questions/56314190

QUESTION

How to remove sub-strings from list lines that start with a certain character sequence and generate an output file

Asked 2018-Nov-26 at 14:47

So here is my task: I have this file.txt with the following text lines:

...

ANSWER

Answered 2018-Nov-26 at 14:45

How about this. Open the input file, read it line per line, substitute 'WARNING ...' by an empty string, and write that to an output file.

Source https://stackoverflow.com/questions/53483448

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

Vulnerabilities

No vulnerabilities reported

Install rgr

You can download it from GitHub.
You can use rgr like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the rgr component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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