molecular biology resources

Lesson Plan for new website
Create polls that you can do during class
A great place to store protocols
Mistakes to avoid when presenting data
Planning to save meta-data
Make a cloud datastore where you can share your results with educators
New Tutorial on RNAseq analysis pipeline in CyVerse
Data carpentry folder structure
Intro to BRIC19 RNAseq experiment
DNA subway Green Line (Preprocessing to counts )
Provide counts table Counts from BRIC19 on MacMini desktop (down load link from CyVerse)
Volcano plots require Log FC & -Log10 P-value
RNAseq normaliation tool DESeq, EdgeR, Voom
RNAseq heat map and PCA tool
Instructions for build your own heatmaps
Deposit figures in slide show Find method to save lists of genes and meta data for report
Copmare and contrast datasets
Shiny Venn diagram
Go analysis tool
Alternative Go Analysis tool
Gene network analysis tool
Compare your lists to the transcriptionfactor data bases
Search for co-expression paterns using BAR
Plot the diurnal expression patterns in different light environments
SUBA tool box (co-expression, subcellular location enrichment)
Single gene
Use this tool to investigate the most interesting gene
Use this to make a graphical report on interesting gene expressoin patterns
Observe phylogenetic tree of gene;r=4:18409846-18411069;t=AT4G39670.1
Explore a single gene
Check if your gene is found in the plant membrane protein database
FASTA file format
Check if ther protein contains any transmembrane domains
Design experiment to test hypothesis
Plant image anlysis software
FlashLapse as a tool for acquiring consitant image quality
Protocols and Trello
Tools for quick graph production
Shiny Box Plot
Shiny GGPlot graph production
Shiny for RootNav
Shiny for RootTace
Online statiscal tool with guide
Alternative Shiny Onlines statiscal tool
Online histograms and related stats
Online interactive figure creation
Eric’s root analysis pipeline
J-filament software for measuring roots / wavy lines
Custom R-codes for analyzing roots / wavy lines
New image analysis pipeline
Root NAV & Other plant image analysis software
The language of RSA = RSML
This software can make example roots to train other software
Deposit of ground truth synethetic images
Archi-DART: New R-Shiny app for root modeling / making graphs
PRIMAL machine learning
Root image analysis pipeline evaluation