| Lesson Plan for new website | |
| Create polls that you can do during class | https://pollev.com/ |
| A great place to store protocols | https://www.protocols.io |
| Mistakes to avoid when presenting data | https://www.biostat.wisc.edu/~kbroman/topten_worstgraphs/ |
| Planning to save meta-data | |
| Make a cloud datastore where you can share your results with educators | http://www.iplantcollaborative.org/ |
| New Tutorial on RNAseq analysis pipeline in CyVerse | https://wiki.cyverse.org/wiki/display/TUT/RNA-seq+Tutorial-+HISAT2%2C+StringTie+and+Ballgown |
| Data carpentry folder structure | |
| Intro to BRIC19 RNAseq experiment | http://www.rnaseqforthenextgeneration.org/profiles/barker.html |
| DNA subway Green Line (Preprocessing to counts ) | https://dnasubway.cyverse.org/ |
| Provide counts table | Counts from BRIC19 on MacMini desktop (down load link from CyVerse) |
| Volcano plots require Log FC & -Log10 P-value | http://moderndata.plot.ly/interactive-volcano-plots-r-plotly/ |
| Transcriptome | |
| RNAseq normaliation tool DESeq, EdgeR, Voom | https://gallery.shinyapps.io/DEApp/ |
| RNAseq heat map and PCA tool | https://kcvi.shinyapps.io/START/ |
| Instructions for build your own heatmaps | http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/heatmap/ |
| Deposit figures in slide show | Find method to save lists of genes and meta data for report |
| Copmare and contrast datasets | |
| Shiny Venn diagram | http://jvenn.toulouse.inra.fr/app/example.html |
| Multi-gene | |
| Go analysis tool | http://plantregmap.cbi.pku.edu.cn/go.php |
| Alternative Go Analysis tool | http://bioinfo.cau.edu.cn/agriGO/analysis.php |
| Gene network analysis tool | http://knetminer.rothamsted.ac.uk/Arabidopsis_thaliana/ |
| Compare your lists to the transcriptionfactor data bases | http://atrm.cbi.pku.edu.cn/ |
| Search for co-expression paterns using BAR | http://bar.utoronto.ca/ExpressionAngler/ |
| Plot the diurnal expression patterns in different light environments | http://diurnal.mocklerlab.org/diurnal_data_finders/new |
| SUBA tool box (co-expression, subcellular location enrichment) | http://suba.live/toolbox-app.html |
| Single gene | |
| Use this tool to investigate the most interesting gene | https://apps.araport.org/thalemine/begin.do |
| Use this to make a graphical report on interesting gene expressoin patterns | https://bar.utoronto.ca/eplant/ |
| Observe phylogenetic tree of gene | http://plants.ensembl.org/Arabidopsis_thaliana/Gene/Compara_Tree?g=AT4G39670;r=4:18409846-18411069;t=AT4G39670.1 |
| Explore a single gene | http://www.megabionet.org/atpid/webfile/query.php |
| Check if your gene is found in the plant membrane protein database | http://aramemnon.uni-koeln.de/request.ep |
| FASTA file format | |
| Check if ther protein contains any transmembrane domains | http://www.cbs.dtu.dk/services/TMHMM-2.0/ |
| Design experiment to test hypothesis | |
| Plant image anlysis software | http://plant-image-analysis.org/ |
| FlashLapse as a tool for acquiring consitant image quality | https://github.com/flashlapsedev/Flashlapse_Build |
| Protocols Astrobotany.com and Trello | |
| Tools for quick graph production | |
| Shiny Box Plot | http://shiny.chemgrid.org/boxplotr/ |
| Shiny GGPlot graph production | https://site.shinyserver.dck.gmw.rug.nl/ggplotgui/ |
| Shiny for RootNav | https://rmtrane.shinyapps.io/RootNav/ |
| Shiny for RootTace | https://rmtrane.shinyapps.io/RootTrace/ |
| Online statiscal tool with guide | http://vassarstats.net/ |
| Alternative Shiny Onlines statiscal tool | http://www.intro-stats.com/ |
| Online histograms and related stats | https://www.wessa.net/rwasp_histogram.wasp |
| Online interactive figure creation | https://plot.ly/~PlotBot/51/control-vs-experimental/ |
| Eric’s root analysis pipeline | |
| J-filament software for measuring roots / wavy lines | http://athena.physics.lehigh.edu/jfilament/download.chy#current |
| Custom R-codes for analyzing roots / wavy lines | https://github.com/eschultzphd/RootMeasurement/blob/master/RootMeasure.R |
| New image analysis pipeline | |
| Root NAV & Other plant image analysis software | http://www.plant-image-analysis.org/api |
| The language of RSA = RSML | http://rootsystemml.github.io/tools/ |
| This software can make example roots to train other software | https://www.biorxiv.org/content/early/2016/12/22/074922 |
| Deposit of ground truth synethetic images | http://www.plant-image-analysis.org/dataset/modelled-root-images |
| Archi-DART: New R-Shiny app for root modeling / making graphs | https://archidart.github.io/ |
| PRIMAL machine learning | https://github.com/plantmodelling/primal |
| Root image analysis pipeline evaluation | https://github.com/guillaumelobet/Root-Image-Analysis-Pipeline-Evaluation/tree/v0.1 |