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