todo.txt

$add data transformation other than log
$add external web apps to chart bottom panel
$add gene cards to external search
$add match case for all queries in TreeSearchQueryConstructionPanel
$add null metadata to missing metadata columns while reading metadata file
$add relatedness to menu
$Adding null values to metadata
$after reading data file add widow to select types of infocolumns
$change default rep to outermost/Let user choose a rep column and based on that get reps. This assumes reps in different samples. 
$Change MI matrix
$check for auto updates
$check joint entropy
$check metadata column names before building tree (handle illegal name exception)
$check MI code
$color volcanoplot
$compute p-val for spearman using fisher from wiki https://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
$delete unused columns in MD
$deleting/removing/shifting columns change hyperlink columns
$does cluster function exclude columns ???
$double stars in project title
$filter last search problems with jtable
$fix open project locate file //works on windows
$fix scatterplot metadata
$handle defaultRpath flag
$Handle missing data
$Horizontal scroll import metadata
$improve clicking on chart point/Push annotations far from mouse to allow click
$improve import list
$improve searching speed
$list intersection and union
$list search or and and not working
$locate tsv files
$mac npd to front
$make "finding samples" interface
$Make links to SRA and GEO databases
$make scatter plot for two selected rows
$manage rangemarkers
$metadata table remove new proj with selected
$metadata view functionality
$MI z values
$move external application option to menu
$move search results together
$plot selected series/features in box plot
$remove blank row from metadata
$Remove correlation columns from main table
$save a list of extra rows in metadata and remove them when project is reopened
$save all properties correlation p vals etc to project
$save main table to file
$save SRA links
$Search in tree metadata
$shift annotation to left of points are on right of chart
$Show p val on mouse hover
$Sort by x axis labels
$spearman corr p value
$spearman correlation slow
$test list intersection
$transform data from chart right click menu
$when saving query, also save match all or match any flag
?add "and" option to quick filter
?Add splash screen/using j exe
?allow changing/selecting info cols while in project. 
?improve pval skip smaller associations
?include gephi graph toolkit
?load gene metadata
?Make table more readable
?Make windows part of project windows
?MCL clustering
?use Lucene for reading files
?use of ND4J
add actions to help buttons
add bar chart
add chart annotator for replicate plot
add data size to plot legends
add grouping var name in corr detail
add java color e.g. https://github.com/rcsb/colorbrewer ?
add mean lines to plot
add p val corection to diff corr
add project info to display project files etc
add pval correction methods
add scroll in annotation table
add separate correlation pane?
add spearman corr for samps
add threshold to all pairwise computation
add utility function to filter out colors that match background of plot
add xml read support for metadata
Allow to add rows in data as function of selected rows e.g. select genes and add avg of those in each sample or all sample as a new row, or select one gene and its avg over all the sample
Allow to hide show series; arrange histogram. make more interactive
allow user to add a short description to correlation column which will be displayed on mouse hover; save the descriptions with project; by default add current data selection, list information in the description;this makes easier to recognize computations
Allows Spliting Sample attributes in MOG e.g. (a1:v1||a2:v2||a3:v3) should add three attribute a1, a2, a3 with values v1, v2, v3
atleast two rows should be selected for scatter plot 
bug in alphanumeric sort main table
build reps column is slow again
change def rep col set to current selected col, only call func if changed
chart fonts and size
check shuff in group when repsmap is data column
combine metadata terms to group expression e.g. tumor+tissue will give liver,normal; liver,tumor; stomach,normal;stomach,tumor etc.
convert to internal frames
create a common class to handle plot functions from different tables
create a filter based on gene expression
dashed vs solid error bar
deal with illegal chars
delete metadata not working
DTP bring to top
execute other R script ask for out file name 
filter corrleation details table by r and pval
fix alphanumeric comparator for case sensitive values
fix cancelling logfc
fix email send without pass
fix shuff in group/order is different
Handle memory efficiently for analyzing runs (cosine sim, etc)
Have chart its own excluded data values; Add refresh options to chart sync with current workspace; Allow to filter in current chart only. 
How error is plotted in avg chart??
improve sample series plot
in pearson corr no pval, if data is missing it skips the cols with missing data. Change this to return 0 if a column is missing for a row.
initialize trivial metadata table is none is given
Invert selection in Dual table panel while editing or creating list//add actions
kruskalWalis test
list merge handle case sensitive names e.g. C15ORF37
make color themes
MI,spearman,PC, test all
mog correlation detail table; remove "load table" function for now
move splitindex to project class
?option to edit metadata
order of groups in line chart, hist etc.
p values histogram
plot as series xaxis label
pvalue doesn't show in list
remove genes from plot once a plot is drawn
remove special chars from data columns	
reset rows update title
revise edit info column function;keep or remove
save correlation matrix as robject
save diff exp res
set plot background in properties
show header name on hover
show list size on hover 
show num of cd used in rep plot metadata
sort boxplots by mean median..
Sort in chart while grouped by metadata
test groupDataIndexbyRepColumn()
Test tree building algorithm 
try plotly
update boxplot/add more options to boxplot interactions/split box plots type by metadata/color by different types categories// add tooltip
$update default rep columns as data is filtered
update tips
$use "feature" instead of genes/rows
user function for transformation;add option to clip -ve values to 0; make a transformation pipeline defined by user which can allow many functions in a defined order on the data
venn diagrams fo correlated genes?
$wrap text in metadta tree/table
$add filter to DE res table
$boxplot options e.g. outliers, mean, tooltip
$add options in all charts. show/hide legend
$Properties -> sample name, header names
$add new diffcorr pipeline frame
take default label axis for all charts
add filter by expression in main table 
add spearman corr to samples
faster filtering of excluded samples while computing DE
legend font
$add menu to DifferentialCorrFrame
histogram tooltips
search genes in volcano plot by metadata
MI validation
fix drag metadata tree problems 
table fonts
$add genecards to external web apps button in line charts
MOG icons in all windows
scaterplot tooltip show series name
Check XML name before saving project
refactor ;remove unused modules and files
Handle duplicate column headers in metadata file
metadata  validation error not showing in MAC
add pval correction to correlation p values
$add holms method to all tables
add validation to meta analysis
permutation test for DiffCorr
diff corr with same feature show 0 p value
corr p value t test
$add p value hist/ correction in all results frames
$permutation test for paired data
differential corr for spearman corr
$test for differential correlation method
$test REF FEM