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SimpleBio

Easy-to-use biological sequence tools working with DNA, RNA and aminoacid sequences.

https://github.com/doctorbetaq/simplebio.jl

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords

amino-acids bioinformatics dna rna
Last synced: 6 months ago · JSON representation ·

Repository

Easy-to-use biological sequence tools working with DNA, RNA and aminoacid sequences.

Basic Info
Statistics
  • Stars: 7
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 4
Topics
amino-acids bioinformatics dna rna
Created about 3 years ago · Last pushed about 3 years ago
Metadata Files
Readme License Citation

README.md

SimpleBio.jl

release license build CodeCov docs docs DOI Stars

Work with biological sequences as simple as a text way!

Features

1. Sequence identification for DNA or RNA by isdna, isrna functions.

2. Work with nucleotides:

  • Function transcript (xtranscript) for transcription of DNA to RNA (xtranscript for DNA with nucleobase not ATCG.)
  • Reverse-compliment sequence using DNArc and RNArc functions.
  • Retro-Transcription of RNA to DNA using RTanscript function.
  • Function RandSeq for generating DNA, RNA or amino acid chains. randdnarna function to generate a dataframe for random DNAs and their transcription.
  • Use the tranlatedna function for translation of dna sequence (also can enter RNA sequence if needed) to amino acid sequence.
  • Primer design tools (in development) #### 3. Sequence alignment with nalign (DNA or RNA) and aalign (for amino acid sequences). #### 4. Outputs are text String that can be used in the further processing!

Tests

SimpleBio has been tested in macos, linux and windows environments with latest julia stable release.

test

Install

To install SimpleBio, type ']' in REPL to enter Pkg mode and type: julia add SimpleBio

Usage

To use SimpleBio, simply type in: julia using SimpleBio

Owner

  • Name: BetaQ
  • Login: doctorbetaq
  • Kind: user
  • Company: WhirlingPlumage studio

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Pang"
    given-names: "Hao-Han"
    orcid: "https://orcid.org/0000-0001-9071-9649"
title: "doctorbetaq/SimpleBio.jl: v0.1.0"
version: v0.2.0
doi: 10.5281/zenodo.7547946
date-released: 2023-01-24

GitHub Events

Total
Last Year

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 271
  • Total Committers: 2
  • Avg Commits per committer: 135.5
  • Development Distribution Score (DDS): 0.465
Past Year
  • Commits: 271
  • Committers: 2
  • Avg Commits per committer: 135.5
  • Development Distribution Score (DDS): 0.465
Top Committers
Name Email Commits
Han H. Pang h****3@g****m 145
BetaQ 9****q 126

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 2
  • Total pull requests: 2
  • Average time to close issues: less than a minute
  • Average time to close pull requests: less than a minute
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 10.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • doctorbetaq (1)
  • JuliaTagBot (1)
Pull Request Authors
  • doctorbetaq (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
juliahub.com: SimpleBio

Easy-to-use biological sequence tools working with DNA, RNA and aminoacid sequences.

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 9.9%
Average: 35.5%
Dependent packages count: 38.9%
Stargazers count: 39.8%
Forks count: 53.5%
Last synced: 7 months ago

Dependencies

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  • julia-actions/julia-processcoverage v1 composite
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.github/workflows/Documenter.yml actions
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  • codecov/codecov-action v3 composite
  • julia-actions/julia-processcoverage v1 composite
  • julia-actions/setup-julia v1 composite
.github/workflows/TagBot.yml actions
  • JuliaRegistries/TagBot v1 composite
.github/workflows/CompatHelper.yml actions
  • julia-actions/setup-julia v1 composite
.github/workflows/test.yml actions
  • actions/checkout v2 composite
  • julia-actions/julia-runtest latest composite
  • julia-actions/setup-julia v1 composite