topiary | Predict mutated T-cell epitopes from sequencing data | Genomics library

by openvax Python Version: v0.0.19 License: Apache-2.0

X-Ray Key Features Code Snippets(2)Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | topiary Summary

topiary is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. topiary 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.

Predict mutation-derived cancer T-cell epitopes from (1) somatic variants (2) tumor RNA expression data, and (3) patient HLA type.

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Support

topiary has a low active ecosystem.

It has 22 star(s) with 9 fork(s). There are 14 watchers for this library.

It had no major release in the last 12 months.

There are 29 open issues and 27 have been closed. On average issues are closed in 56 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of topiary is v0.0.19

Quality

topiary has no bugs reported.

Security

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

License

topiary 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

topiary releases are available to install and integrate.

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

Predict Epitopes from the given arguments
Apply filter to collection
Filter variants based on gene expression
Predict from variants
Create an argument parser
Adds filter options to the argument parser
Add command line arguments to an arg parser
Adds error arguments to the argument parser
Load data into a dictionary
Write output columns
Predict from given sequences
Parse command line arguments

Get all kandi verified functions for this library.

topiary Key Features

No Key Features are available at this moment for topiary.

topiary Examples and Code Snippets

Topiary,Example

Python

Lines of Code : 13

License : Permissive (Apache-2.0)

Copy

./topiary \
  --vcf somatic.vcf \
  --mhc-predictor netmhcpan \
  --mhc-alleles HLA-A*02:01,HLA-B*07:02 \
  --ic50-cutoff 500 \
  --percentile-cutoff 2.0 \
  --mhc-epitope-lengths 8-11 \
  --rna-gene-fpkm-tracking-file genes.fpkm_tracking \
  --rna-m

Topiary,Installation

Python

Lines of Code : 3

License : Permissive (Apache-2.0)

Copy

pip install topiary

pyensembl install --release 81 --species human

pyensembl install --release 75 --species human

Community Discussions

Trending Discussions on topiary

Extract last specified number of sentences in r

Regex to extract all text from a specified pattern till end of string in r

Text summary in R for multiple rows

QUESTION

Extract last specified number of sentences in r

Asked 2020-Oct-23 at 04:06

I am now trying to extract the three sentences in a text string using r

this post deals with a similar problem, Extracting sentences in R and looks like that the regex to identify sentence is something like: '.*"(.*)".*' but i am unable to apply it to

Create an example:

...

ANSWER

Answered 2020-Oct-23 at 03:11

I would suggest splitting your data into sentences and keep one row for each sentence. For this you need to define what is a sentence. We can split the text when there is a full stop followed by a whitespace (\\s) or newline (\n) or tab (\t) or opening square bracket ([) (Or probably just full stop is enough). Once we do that we can get last 3 sentence or first 2 sentence easily.

Source https://stackoverflow.com/questions/64493252

QUESTION

Regex to extract all text from a specified pattern till end of string in r

Asked 2020-Oct-23 at 02:48

I am trying to extract all the text from the word "Conclusion" till end of text using stringr

...

ANSWER

Answered 2020-Oct-22 at 23:37

We can use the pattern to match 'Conclusion' followed by ':' and a space or 'Conclusion' followed by space and next line and match all the characters after that (.*)

Source https://stackoverflow.com/questions/64491816

QUESTION

Text summary in R for multiple rows

Asked 2020-Oct-03 at 16:02

I have a set of short text files that I was able to combine into one datatest so that each file is in a row.

I am trying to summarize the content using the LSAfun package using the generic function argument genericSummary(text,k,split=c(".","!","?"),min=5,breakdown=FALSE,...)

This works very well for single text entry, however it does not in my case. In the package explanation it says that the text input should be "A character vector of length(text) = 1 specifiying the text to be summarized".

Please see this example

...

ANSWER

Answered 2020-Oct-03 at 16:02

Check class(dd$text). It's a factor, which is not a character.

The following works:

Source https://stackoverflow.com/questions/64185994

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

Vulnerabilities

No vulnerabilities reported

Install topiary

You can install Topiary and all of the libraries it depends on by running:.

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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