I'm helping a scientist find a suitable tool for searching in their cell-gene-expression database with 20000genes and 3700 cells (will increase). The data is just tab-separated.
cell1 cell2 cell3
Gene1 0 3 1
Gene2 2 5 14
Gene3 5 0 3
One needs to search in this database, for e.g. which cells have expressed>4 on Gene1 and Gene3? Also visualization of the result will be important and other types of add-on searches/comparisons.
My alternatives are building a tool from scratch in perhaps matlab/python/R, or using some BI-tool like Tableau/Spotfire, or looking for some tool at bioconductor.org.
I was wondering if anyone knows of any other tool or database of tools with this functionality.
If you simply want to get all genes with a score >x, you can probably build a simple awk script, something like:
awk '{if ( $4 >= 14) print $0, "cell3"}' yourfile.txt
Hello
Sorry if I did not get correctly what do You need... but probably this will work (see attachment)?
I understand that it is not the best way and it will only work if You are looking between pair of genes. In this case You just reorder the genes by pairs and copy/paste formula. It is annoying, but if You have a doable number of genes probably it will be easier than right a script? The obtained new data table can be visualized as a heat-map.
If You need to compare each gene with each I would use loop in R, as You said.
Both ways are possible. Awk is time effective and excel is simple.
But I'm not sure how good awk is for visualisation purposes and building gui. It would be possible to run an awk script and then do visualization in another program. But the end users of this tool is (according to themselves) programming-illiterates, so I think it needs to be a gui or very simple functions.
And I'd rather not build a tool/function inside excel since the number of cells will increase (right now 3700) and the number of genes is about 20000. Excel is already laggy.
This feels like a very common task, which is why I'm hoping for an already made tool/package. I'll take a look at bioconductor.org and see if there is a tool or if I need to build it myself in R.
Thank you!
Do you know about GENE-E? It allows you to import delimited text files and has some nice built-in visualization features.
http://www.broadinstitute.org/cancer/software/GENE-E/
Try the TIGR MEV tool (multi experiment viewer). It can import data from tab separated files, though I am not sure how well it handles your 3700 columns.
GENE-E seems good and simple to load data. I'm having some problems with it on windows 8 though, and (on win7) it took a long time to load. But looked good, so will keep looking at it's features.
TIGR MEV tool was intuitive too but got full heap-space, so I guess its my the large data.
Thanks!
Try one gui channel
It use R, but is user friendly
http://bioconductor.org/packages/release/bioc/html/oneChannelGUI.html
If you decide to build a custom tool with R, check out the Shiny package to easily build a user-friendly web app. The non-bioinformatic researchers in your group would definitely appreciate it.
OneGuiChannel seems to require certain dataformats and does not seem to have adaptive formating as in GENE-E. Formating the files will be a time investment in itself.
I've tried all tools, and they were all great suggestions. Now I've started to using python and R.
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