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C7. Use command-line bioinformatics tools and write simple computer scripts: Most biological datasets (e.g., genomic and proteomic sequences, BLAST results, RNASeq and resulting differential expression data) are available as text files; the most powerful and dynamic way to interact with these datasets is through the command line or shell scripting. Students should be able to manipulate their own data and to create and modify complex data processing and analysis workflows.

  • Run BLAST using command line options
  • Build and run statistical analyses using R or Python scripts
  • Write simple shell scripts to manipulate files

All Categories (1-9 of 9)

  1. An Introduction to the R Programming Environment

    02 Jun 2021 | Teaching Materials | Contributor(s):

    By K. A. Garrett1, P. D. Esker1, A. H. Sparks1

    Kansas State University

    An online module introducing students and biologists to R, published in American Phytopathological Society

    https://qubeshub.org/publications/1002/?v=2

  2. A Critical Guide to BLAST

    04 Dec 2020 | Teaching Materials | Contributor(s):

    By Teresa Attwood1, GOBLET Foundation

    The University of Manchester, Manchester, UK

    This Critical Guide in the Introduction to Bioinformatics series provides an overview of the BLAST similarity search tool, briefly examining the underlying algorithm and its rise to popularity.

    https://qubeshub.org/publications/2172/?v=1

  3. A Critical Guide to Unix

    04 Dec 2020 | Teaching Materials | Contributor(s):

    By Teresa Attwood1, GOBLET Foundation2

    1. The University of Manchester, Manchester, UK 2. Global Organisation for Bioinformatics Learning, Education & Training

    This Critical Guide in the Introduction to Bioinformatics series briefly introduces the Unix Operating System, and provides a subset of some of the most helpful and commonly used commands....

    https://qubeshub.org/publications/2162/?v=1

  4. Introduction to UNIX command line

    22 Jan 2020 | Teaching Materials | Contributor(s):

    By Serghei Mangul1, Kristen Butela2, Michael Sierk3, Lihua Stefan

    1. University of California - Los Angeles 2. University of Pittsburgh 3. Saint Vincent College

    A laboratory module for an upper-level undergraduate biology course in which students will be able to carry out simple tasks using the Unix command-line environment.

    https://qubeshub.org/publications/731/?v=2

  5. A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!

    07 Jun 2019 | Teaching Materials | Contributor(s):

    By Rachael St. Jacques1, Max Maza1, Sabrina Robertson2, Guoqing Lu3, Andrew Lonsdale4, Ray A Enke5

    1. Department of Biology, James Madison University 2. Department of Psychology & Neuroscience, University of North Carolina at Chapel Hill 3. Department of Biology and School of Interdisciplinary Informatics, University of Nebraska Omaha 4. ARC Centre of Excellence in Plant Cell Walls, Melbourne University 5. James Madison University

    This resource is a fun computer-based intro to command line programming. The activity takes FASTQ NGS data files and runs a fun program called FASTQE.

    https://qubeshub.org/publications/1092/?v=2

  6. A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!

    28 Feb 2019 | Teaching Materials | Contributor(s):

    By Rachael St. Jacques1, Max Maza1, Sabrina Robertson2, Guoqing Lu3, Andrew Lonsdale4, Ray A Enke5

    1. Department of Biology, James Madison University 2. Department of Psychology & Neuroscience, University of North Carolina at Chapel Hill 3. Department of Biology and School of Interdisciplinary Informatics, University of Nebraska Omaha 4. ARC Centre of Excellence in Plant Cell Walls, Melbourne University 5. James Madison University

    This resource is a fun computer-based intro to command line programming. The activity takes FASTQ NGS data files and runs a fun program called FASTQE.

    https://qubeshub.org/publications/1092/?v=1

  7. Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

    04 Jan 2019 | Teaching Materials | Contributor(s):

    By Mark Phillip Peterson1, Jacob T Malloy2, Vincent P Buonaccorsi2, James H Marden3

    1. Viterbo University 2. Juniata College 3. Pennsylvania State University

    This lesson plan was created to teach RNAseq analysis as a part of GCAT-SEEK network. It is provided here, both in finished form and with the modifiable source code, to allow flexible adaptation to...

    https://qubeshub.org/publications/1005/?v=1

  8. An Introduction to the R Programming Environment

    04 Jan 2019 | Teaching Materials | Contributor(s):

    By K. A. Garrett1, P. D. Esker1, A. H. Sparks1

    Kansas State University

    An online module introducing students and biologists to R, published in American Phytopathological Society

    https://qubeshub.org/publications/1002/?v=1

  9. Introduction to UNIX command line

    31 Jul 2018 | Teaching Materials | Contributor(s):

    By Serghei Mangul

    University of California - Los Angeles

    These are materials for a Unix workshop with hands-on examples that requires no prior knowledge of Unix or programming.

    https://qubeshub.org/publications/731/?v=1

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