Lesson Plan for new website |
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Create polls that you can do during class |
https://pollev.com/ |
A great place to store protocols |
https://www.protocols.io |
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Mistakes to avoid when presenting data |
https://www.biostat.wisc.edu/~kbroman/topten_worstgraphs/ |
Planning to save meta-data |
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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 |
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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/ |
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Transcriptome |
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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/ |
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Deposit figures in slide show |
Find method to save lists of genes and meta data for report |
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Copmare and contrast datasets |
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Shiny Venn diagram |
http://jvenn.toulouse.inra.fr/app/example.html |
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Multi-gene |
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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 |
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Single gene |
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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 |
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FASTA file format |
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Check if ther protein contains any transmembrane domains |
http://www.cbs.dtu.dk/services/TMHMM-2.0/ |
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Design experiment to test hypothesis |
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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 |
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Tools for quick graph production |
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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/ |
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Eric’s root analysis pipeline |
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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 |
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New image analysis pipeline |
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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 |