biopsy | Biopsy - the Bioinformatic Optimisation System | Machine Learning library

by blahah Ruby Version: v0.1.0a License: MIT

X-Ray Key Features Code Snippets Community Discussions(9)Vulnerabilities Install Support

kandi X-RAY | biopsy Summary

biopsy is a Ruby library typically used in Artificial Intelligence, Machine Learning applications. biopsy has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

Biopsy - the Bioinformatic Optimisation System

Support

Quality

Security

License

Reuse

Support

biopsy has a low active ecosystem.

It has 17 star(s) with 3 fork(s). There are 3 watchers for this library.

It had no major release in the last 12 months.

There are 6 open issues and 6 have been closed. On average issues are closed in 108 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of biopsy is v0.1.0a

Quality

biopsy has 0 bugs and 0 code smells.

Security

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

biopsy code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

biopsy is licensed under the MIT License. This license is Permissive.

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

Reuse

biopsy releases are available to install and integrate.

Top functions reviewed by kandi - BETA

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

generate parameters
Run the optimisation
Runs the results of the given output .
Sets up the results of the thread
Loads the objectives of the objective .
Runs the optimisation of a task .
Cleans up any necessary files
Stores the target configuration .
Runs the candidate for a candidate .
creates a new mate

Get all kandi verified functions for this library.

biopsy Key Features

No Key Features are available at this moment for biopsy.

biopsy Examples and Code Snippets

No Code Snippets are available at this moment for biopsy.

Community Discussions

Trending Discussions on biopsy

How can I filter data in spss by multiple conditions

How best to use R to reshape dataframe from long to wide and combine values

How to remove single alphabet and dot from sentence using regex

Dplyr - choosing value in column based on lowest value in other column in R

Subtracting a date in one column from previous unique date in another column in R

From the following tables, write a query to get the histogram of specialties of the unique physicians who have done the procedures

Choosing forward propagating observation in R

Using case and group-by at the same time

Pyton Regular Expressions-Find all sentences starting with a hyphen character and put them in a list

QUESTION

How can I filter data in spss by multiple conditions

Asked 2021-Oct-28 at 08:34

I am working with a large dataset on SPSS. I have certain inclusion and exclusion criteria for a research project, but I am unsure how to filter the data by complex conditions.

For example, I want to include cases that satisfy specific criteria:

Inclusion: Had surgery, cancer was in the oropharynx, cancer was in the oral cavity

Exclude: has metastatic disease, no biopsy done, has missing data on survival and margin status.

The variables given to me are complicated. For example the variable for the primary site of cancer is a list of strings which describe different parts on the body. I would have to recode this into being oropharynx or oral cavity and then I only want cases with either of those sites.

What is the best systematic approach using syntax? Should I use Do IF, IF ELSE statements? or filter by?

Im not sure how to filter by all of these conditions in the syntax editor

...

ANSWER

Answered 2021-Oct-28 at 08:34

Best to calculate a new variable with all the conditions, then use it to filter.

In the following example, variable filt will receive value 1 for cases that have all the conditions, and 0 for those that don't:

Source https://stackoverflow.com/questions/69750095

QUESTION

How best to use R to reshape dataframe from long to wide and combine values

Asked 2021-Oct-22 at 02:28

I have a dataframe of about 2000 rows and 3 columns. In essence, I want to reshape this dataframe to be wider than longer. This is an example of my current data:

ID Procedure Date D55 Sedation 01/01/2001 D55 Excision 01/01/2001 D55 Biopsy 01/01/2001 A66 Sedation 02/02/2001 A66 Excision 02/02/2001 T44 Sedation 03/03/2001 T44 Biopsy 03/03/2001 T44 Sedation 04/04/2001 T44 Excision 04/04/2001 G88 Sedation 05/05/2001 G88 Biopsy 05/05/2001 G88 Sedation 06/06/2001 G88 Excision 06/06/2001 G88 Sedation 07/07/2001 G88 Re-excision 07/07/2001

I want the each row to be one line for the ID, so I'd want to create something like this:

ID Date 1 Procedure(s) Date 2 Procedure(s) Date 3 Procedure(s) D55 01/01/2001 Sedation, Excision, Biopsy A66 02/02/2001 Sedation, Excision T44 03/03/2001 Sedation, Biopsy 04/04/2001 Sedation, Excision G88 05/05/2001 Sedation, Biopsy 06/06/2001 Sedation, Excision 07/07/2001 Sedation, Re-excision

The majority of IDs all have the same date, but different procedures documented. There are a handful that came in for further procedures on subsequent dates. I can't see any that came in for more than 3 different dates, but a way to count the dates documented per ID would be useful.

I've tried using cast and dcast so far, but I'm not really getting anywhere. I'm very new to R, so any help would be greatly appreciated! Thanks for reading.

...

ANSWER

Answered 2021-Oct-22 at 02:28

library(tidyverse)
df %>%
  group_by(ID, Date) %>%
  summarize(Procedure = paste0(Procedure, collapse = ", ")) %>%
  mutate(col = row_number()) %>%
  ungroup() %>%
  pivot_wider(names_from = col, values_from = c(Date, Procedure))

Source https://stackoverflow.com/questions/69669640

QUESTION

How to remove single alphabet and dot from sentence using regex

Asked 2021-Oct-19 at 14:47

 sentence = "Diagnosis: B. 
 Prostate, Left Lateral Mid, Core Biopsy: - Prostatic adenocarcinoma, Gleason's score 3+3=6/10 - Single focus of carcinoma measures 0.5 mm (involves 1 of 1 core fragment and up to 5% of individual core volume) - Prostatic intraepithelial neoplasia (PIN high grade C. 
 Prostate, Left Lateral Apex, Core Biopsy: - Prostatic "

Required solution: Diagnosis: Prostate, Left Lateral Mid, Core Biopsy: - Prostatic adenocarcinoma, Gleason's score 3+3=6/10 - Single focus of carcinoma measures 0.5 mm (involves 1 of 1 core fragment and up to 5% of individual core volume) - Prostatic intraepithelial neoplasia (PIN high grade 
     Prostate, Left Lateral Apex, Core Biopsy: - Prostatic

...

ANSWER

Answered 2021-Oct-19 at 14:47

You are on the right track with something based on regex. I think you can use re.sub() and a simple pattern that expects whitespace then a alpha character and a period.

Source https://stackoverflow.com/questions/69632491

QUESTION

Dplyr - choosing value in column based on lowest value in other column in R

Asked 2021-Oct-08 at 21:38

I am currently working on a dataset with multiple biopsies per patient ID. I need to find the biopsy result closest to a specific date (individual per patient). A dummy dataset can be seen below

...

ANSWER

Answered 2021-Oct-08 at 11:27

You can get index of minimum absolute value of difference between the dates for each group.

Source https://stackoverflow.com/questions/69495031

QUESTION

Subtracting a date in one column from previous unique date in another column in R

Asked 2021-Aug-06 at 21:05

I have a dataframe as following:

...

ANSWER

Answered 2021-Aug-06 at 21:05

A tidyverse option using tidyr::fill.

Source https://stackoverflow.com/questions/68685108

QUESTION

From the following tables, write a query to get the histogram of specialties of the unique physicians who have done the procedures

Asked 2021-Apr-23 at 20:19

From the following tables, write a query to get the histogram of specialties of the unique physicians who have done the procedures but never did prescribe anything.

Patient treatment table

...

ANSWER

Answered 2021-Apr-23 at 20:19

I threw this Fiddle together: http://sqlfiddle.com/#!9/2481c3/4/0

Does this query turn up what you're looking for?

Source https://stackoverflow.com/questions/67234695

QUESTION

Choosing forward propagating observation in R

Asked 2021-Mar-13 at 18:58

I am working with a dataset like this: There is the participant ID and then there is the date of the exam and the date of biopsy. There are multiple observations per participant.

The dataset looks like this:

...

ANSWER

Answered 2021-Mar-13 at 18:58

If I am understanding the problem correctly, something like this should work:

Source https://stackoverflow.com/questions/66616721

QUESTION

Using case and group-by at the same time

Asked 2020-Aug-26 at 02:26

I want to use case in SQL, but also using the right group by

...

ANSWER

Answered 2020-Aug-26 at 01:36

You need to repeat the case in the group by, I think:

Source https://stackoverflow.com/questions/63589275

QUESTION

Pyton Regular Expressions-Find all sentences starting with a hyphen character and put them in a list

Asked 2020-Jul-10 at 18:13

I have a text file i want to parse through and put the questions and options into a question and options list

example text: [UPDATED THE EXAMPLE TEXT TO INCLUDE ALL THE TYPES OF VARIATIONS IN THE QUESTION TYPES AND OPTIONS]

...

ANSWER

Answered 2020-Jul-10 at 15:28

Simple:

Source https://stackoverflow.com/questions/62836993

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

Vulnerabilities

No vulnerabilities reported

Install biopsy

You can download it from GitHub.
On a UNIX-like operating system, using your system’s package manager is easiest. However, the packaged Ruby version may not be the newest one. There is also an installer for Windows. Managers help you to switch between multiple Ruby versions on your system. Installers can be used to install a specific or multiple Ruby versions. Please refer ruby-lang.org for more information.

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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