@Alan__Collins

Senior Bioinformatician at IHRC Inc.

 Georgia, USA
github.com/Alan-Collins
Joined November 2017
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The CRISPR Comparison Toolkit (CCTK) is now published in @CRISPRjournal with @RachelJWhitaker! doi.org/10.1089/crispr.2022.… Github github.com/Alan-Collins/CRIS… Conda anaconda.org/bioconda/cctk Read the docs crispr-comparison-toolkit.re… 1/3
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Anybody out there working in comparative CRIPSR biology/informatics? Check out this tool - produces incredible graphics and is really helpful for analysis!👇
Alan Collins@Alan__Collins18 Jul 2023
The CRISPR Comparison Toolkit (CCTK) is now published in @CRISPRjournal with @RachelJWhitaker! doi.org/10.1089/crispr.2022.… Github github.com/Alan-Collins/CRIS… Conda anaconda.org/bioconda/cctk Read the docs crispr-comparison-toolkit.re… 1/3
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See the thread associated with the preprint for a description of what CCTK can do xitter.cf/Alan__Collins/status/1… and check out the releases page to see the new features and bug fixes since CCTK was first released almost a year ago. 2/3
Alan Collins@Alan__Collins1 Aug 2022
I’m excited to announce a new preprint with @RachelJWhitaker! We developed a command line toolkit for the identification and analysis of CRISPR arrays, called the CRISPR Comparison ToolKit (CCTK). A thread about what it can be used for: 1/15
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Thank you to reviewers and users who submitted bug reports for helping to improve CCTK over the last year! We hope to continue to improve it moving forward! 3/3
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I’m excited to announce a new preprint with @RachelJWhitaker! We developed a command line toolkit for the identification and analysis of CRISPR arrays, called the CRISPR Comparison ToolKit (CCTK). A thread about what it can be used for: 1/15
bioRxiv@biorxivpreprint1 Aug 2022
CRISPR comparison toolkit (CCTK): Rapid identification, visualization, and analysis of CRISPR array diversity biorxiv.org/cgi/content/shor… #bioRxiv
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You can visualize how many targets each spacer has (or other data), by using custom colour schemes for CCTK tools. Here is the CRISPRdiff plot with spacers coloured according to the number of targets we found. 14/15
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We hope that CCTK will be useful for your research! CCTK can be installed via conda (anaconda.org/bioconda/cctk), source code is available on GitHub (github.com/Alan-Collins/CRIS…), and documentation is available on RTD (crispr-comparison-toolkit.re…) 15/15
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My Former PhD student Giulia Orazi's minireview "It Takes a Village”: Mechanisms Underlying Antimicrobial Recalcitrance of Polymicrobial Biofilms" made the Top 5 cited papers in JB list! @DartCF pubmed.ncbi.nlm.nih.gov/3154…

"It Takes a Village": Mechanisms Underlying Antimicrobial Recalcitrance of Polymicrobial Biofilms -...

Chronic infections are frequently caused by polymicrobial biofilms. Importantly, these infections are often difficult to treat effectively in part due to the recalcitrance of biofilms to antimicrob...

pubmed.ncbi.nlm.nih.gov
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