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https://github.com/acvill/crisprviewr

an R package for repairing, comparing, and visualizing CRISPRs across environmental datasets

https://github.com/acvill/crisprviewr

Science Score: 26.0%

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    Found 2 DOI reference(s) in README
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    Low similarity (11.0%) to scientific vocabulary

Keywords

bioinformatics crispr ggplot2 metagenomics tidyverse visualization
Last synced: 5 months ago · JSON representation

Repository

an R package for repairing, comparing, and visualizing CRISPRs across environmental datasets

Basic Info
  • Host: GitHub
  • Owner: acvill
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 652 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Topics
bioinformatics crispr ggplot2 metagenomics tidyverse visualization
Created over 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

CRISPRviewR: an R package for repairing, comparing, and visualizing CRISPRs across environmental datasets

CRISPR23_oralmicrobiomes_bgwhite_preview5

Background

CRISPRviewR uses the output from minCED to associate, compare, and visualize CRISPR arrays across environmental samples. To get a sense for the shape of minCED data, check out the example files.

ctSkennerton/minced - GitHub

This package relies on the functions of other packages for data cleaning and plotting, including the following: - dplyr, ggplot2, and other components of the tidyverse - Biostrings - ggpubr - ggnewscale - ggseqlogo

Installation

devtools::install_github("acvill/CRISPRviewR") RStudio users may have to run RStudio with administrator privileges for the devtools installation to work.

Example

Please see the CRISPRviewR vignette for a suggested workflow.

Caveat emptor

The CRISPRviewR functions make no assumptions about the completeness of the CRISPR arrays annotated by minCED or the structure of the underlying assembly. In that regard, users of CRISPRviewR should be aware of the following possibilities.
1. Due to their abundance of direct repeats, CRISPR arrays are often misassembled, particularly in the absence of sufficient coverage. 2. minCED does not predict orientation of arrays, which requires either identification of cas genes or the annotation of a leader sequence. Therefore, CRISPRviewR plots may be backwards with respect to the direction of transcription. If this is a problem, use a tool like CRISPRleader to get strand orientation, then export your plots and invert manually. 3. For fragmented assemblies, CRISPR arrays may occur at contig boundaries. 4. For time-course metagenomic assemblies, differences in CRISPR array structure through time may be attributed to standing variation as opposed to array expansion / recombination. 5. minCED relies on CRISPR Recognition Tool (CRT) to detect CRISPR repeats. The CRT algorithm requires repeats to be identical, and this stringency can lead to the misassignment of portions of repeat sequences to spacers. Consider setting fix_repeats = TRUE when calling read_minced() to address this issue. See "Fix truncated repeats" in the vignette and my related blog post for more details.

Bugs and notes

  • CRISPRviewR has only been tested with the output from minCED v0.4.2
  • If you find a bug or want to suggest a new feature, please open an issue or make a pull request.

Owner

  • Name: Albert Vill
  • Login: acvill
  • Kind: user
  • Location: Connecticut, USA

PhD in metagenomics. Currently in the Turner Lab at Yale

GitHub Events

Total
  • Issues event: 4
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 8
Last Year
  • Issues event: 4
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 8

Issues and Pull Requests

Last synced: 5 months ago

All Time
  • Total issues: 3
  • Total pull requests: 0
  • Average time to close issues: 19 days
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.67
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 0
  • Average time to close issues: 19 days
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.67
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • acvill (2)
  • emilyjunkins (1)
Pull Request Authors
Top Labels
Issue Labels
bug (1) enhancement (1)
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 4.1 depends
  • Biostrings >= 2.64 imports
  • S4Vectors >= 0.34 imports
  • dplyr >= 1.0 imports
  • ggnewscale >= 0.4 imports
  • ggplot2 >= 3.3 imports
  • ggpubr >= 0.4 imports
  • ggseqlogo >= 0.1 imports
  • purrr >= 0.3 imports
  • readr >= 2.1 imports
  • stats >= 4.2 imports
  • stringr >= 1.4 imports
  • tibble >= 3.1 imports
  • tidyr >= 1.2 imports
  • knitr * suggests
  • rmarkdown * suggests