Monthly Archives: August 2015

Pathway Analysis for RNAseq Data – NGS2015

Presentation by Dr. Asela Wijeratne, Ohio State University at Molecular and Celluar Imaging Center. Research interests in co-expression networks during pathogen attack in agricultural plant species to identify regulatory genes. Today: Different approaches for pathway analysis, statistical approaches, example using … Continue reading

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RNAseq differential expression analysis – NGS2015

Dr. Meeta Mistry, Harvard School of Public Health, Bioinformatics Core See awesome workflows available from facility: https://bcbio-nextgen.readthedocs.org/en/latest/ HSPH Bioinformatics Core offers regular short courses, Introduction to RNA-Seq, ChIP-seq, Unix and R courses as well as in-depth NGS courses, Software and … Continue reading

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Reproducible Research Using Rmarkdown – NGS2015 Week 3

Tutorial by Marian Schmidt, PhD candidate at the University of Michigan and Software Carpentry instructor. Fun presentation! Have¬†used knitR and Rmarkdown for analysis script files before, but I didn’t even know that github could be accessed through the RStudio interface. … Continue reading

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Genome Assembly – Week 3 NGS 2015

Great experience participating in genome assembly tutorial by Dr. Lex Nederbragt, Norwegian Sequencing Centre: https://github.com/lexnederbragt http://flavors.me/flxlex https://flxlexblog.wordpress.com/ https://www.flickr.com/photos/lpcohen/20850074396/ Notes below, feel free to comment and correct! Atlantic cod genome assembly! http://www.nature.com/nature/journal/v477/n7363/full/nature10342.html Ensembl annotation: http://www.ensembl.org/Gadus_morhua/Info/Index http://www.aquagenome.uio.no/ Experience switching to computational work … Continue reading

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Multivariate Tests with NGS Data and Visualization in R – Week 3 NGS 2015

Dr. Ryan Williams, postdoc at Iowa State leads tutorial on R visualizations with multivariate statistical approaches for RNAseq data. Traditionally, multivariate stats approaches used for community ecology. Following¬†are my patchy notes from the tutorial. Please feel free to comment and … Continue reading

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