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GCAT-SEEK Eukaryotic Genomics Workshop Manual

Developed by Dr. Vince Buonaccorsi at Juniata College, the GCAT-SEEK Eukaryotic Genomics Workshop Manual consists of seven chapters that cover genome assembly, gene annotations, and variant calling:

  1. Genome assembly I: Quality control with FastQC and Trimmomatic
  2. Genome assembly II: Assembly size estimation and k-mer graphs
  3. Genome assembly III: Assembly algorithms
  4. Genome annotation with Maker I: Overview and repeat finding
  5. Genome annotation with Maker II: Whole genome analysis
  6. Whole genome annotation: Miscellaneous methods
  7. SNP calling and interpretation

 

CourseSource Publication

 

Buonaccorsi, V.P., Hamlin, D., Fowler, B., Sullivan, C., and Sickler, A. 2017. An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching. CourseSource. https://doi.org/10.24918/cs.2017.1

  1. Abyss
  2. assembly algorithms
  3. BUSCO
  4. genome assembly
  5. Maker
  6. Orthofinder
  7. Redundans

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Comprehensive list of color palettes available in r

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  1. color
  2. palette

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The viridis color palettes

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  1. color
  2. palette

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Color Brewer 2.0: Color advice for maps

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  1. color
  2. palette

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A Wes Anderson color palette for R

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  1. color
  2. palette

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Colors in R

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  1. color
  2. STHDA

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R color cheatsheet

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by Melanie Frazier

  1. color

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R Colors

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  1. color

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Neuroscience Core Concepts

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Jacob Shreckengost onto Resources for Teaching with Cases and PBL
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Science in the Classroom

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Fundamentals of Neuroscience

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laptop use hinders learning

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NSF INCLUDES: Report to the Nation

Report on outcomes of NSF INCLUDES program. NSF INCLUDES (Inclusion across the Nation of Communities of Learners of Underrepresented Discoverers in Engineering and Science) is a comprehensive national initiative designed to enhance U.S. leadership in science, technology, engineering and mathematics (STEM) discoveries and innovations by focusing on diversity, inclusion and broadening participation in these fields at scale. The vision of NSF INCLUDES is to catalyze the STEM enterprise to collaboratively work for inclusive change, which will result in a STEM workforce that reflects the diversity of the Nation. 

  1. diversity
  2. inclusion
  3. stem

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Keeping Data Science Broad Report

A report summarizing a series of webinars and workshops to garner community input into pathways for keeping data science education broadly inclusive by bridging the digital and data divide among higher education institution types.

  1. data science
  2. diversity
  3. higher education
  4. inclusion

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Brain Science Podcast

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Jacob Shreckengost onto Resources for Teaching with Cases and PBL
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Neurotoxins lists

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High Content Q&A videos

https://www.thermofisher.com/us/en/home/life-science/cell-analysis/cellular-imaging/high-content-screening/hca-q-and-a.html

  1. high-content
  2. videos

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Bioimage Informatics Activity - Julian, D. 2018

  1. ImageJ
  2. Imaging
  3. Quantitative reasoning

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Writing Case Notes

Here is the description of what should be included in Case Notes

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PB and Case Readings and References

First documents has links to articles about cases and PBL including an annotated bibliography link!!

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Materials for Writng a Case

The collection contains handouts and powerpoints about writing cases

  1. cases and pbl
  2. writing cases

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DATASET Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Dataset for case study

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Leigh Ann Samsa onto scRNAseq Analysis Resources
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Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Original paper for case study dataset.

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Granatum

GUI students will use to visualize data. 

"Without a single line of programming code, users can click through the pipeline, setting parameters and visualizing results via the interactive graphical interface. Granatum conveniently walks users through various steps of scRNA-Seq analysis. It has a comprehensive list of modules, including plate merging and batch-effect removal, outlier-sample removal, gene-expression normalization, imputation, gene filtering, cell clustering, differential gene expression analysis, pathway/ontology enrichment analysis, protein network interaction visualization, and pseudo-time cell series construction." Zhu et al. Genome Medicine 9:108. doi:10.1186/s13073-017-0492-3

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Leigh Ann Samsa onto scRNAseq Analysis Resources
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Hot Spot Epidemiology

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