Dear Community,
Please take a look at MicroScope: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1260-x
MicroScope is a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data, including integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network visualization.
To use MicroScope, please visit: http://microscopebioinformatics.org
For developers, MicroScope source code is available at: https://github.com/Bohdan-Khomtchouk/Microscope
MicroScope is free software (released under the GNU General Public License) and you are welcome (and encouraged) to contribute to it. Please submit any bug reports here: https://github.com/Bohdan-Khomtchouk/Microscope/issues.
Please feel free to get in touch via Github, or here on Biostars.
Best regards,
Bohdan Khomtchouk
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I broke something using the demo data :/
Hi John,
You have to run stats first (i.e., the DE analysis):
Can those tabs be kept grayed out until a user follows a logical analysis sequence?
The software guides you to the next step(s) in the analysis using little pop-up messages within the tabs. As such, you're going left to right naturally and, if you decide to start all the way to the right (e.g., Network Analysis), you will be redirected back to where you should be starting. Long story short: MicroScope is designed to make it impossible to follow an illogical analysis sequence ;)
Got that but then how did @John manage to get that error? Did he jump directly to the third tab or went from first to third tab?
That's a really good question, I'm hoping he can let me know so that I can fix any potential bug here. That error should not have appeared if you ran the analysis in sequence. And, even if you didn't run the analysis in sequence, you should've gotten little pop-up messages about it in the tab panels.
Ah, ok, got it to work now that I see i'm supposed to click into the non-control samples box to find them. I didn't know it was a drop-down so i didn't put anything in there. I don't have any JS blockers or weird mods other than i'm running Chromium rather than Chrome/FF/etc. I'm also not getting any popups at all, which is probably related.
So to get the error i just downloaded the data, then uploaded the data, then, err. I think i'll do a video -_-; https://vimeo.com/184043174
When i do get it to work however, your onChange on your form needs a delay/debounce, because if you have 9 things in your non-control samples, and then you want to delete all of them, you have to make 8 intermediary heatmaps first, and they all get stacked up. Otherwise I think this site/tool is pretty awesome :) Lots of good ideas and design decisions.
Yes, you need to first specify the non-control (i.e., experimental samples) and then click Run Statistics. The DE analysis tab tells you this explicitly in the tab panel (this is what I meant by "pop-up"):
Likewise, if you look at what the Heatmap tab tells you at this point, you'll see that you need to run DE analysis first:
Right, I got that and i said that just above the video link. It's obvious when you know that empty white box is a drop down, but i didn't know that at first. I just made the video to show you how i got the error because you asked and i don't see any popups. I'll take it down now that you know the issue and hopefully can fix it.
Hey on an unrelated note, did you really publish 16 times this year according to your Google Scholar? That's awesome man :)
Thanks! Yeah, it's been a good year for me, John :) Hey btw, can you maybe be so kind as to post your Vimeo video with a little walkthrough. I thought you did a really good job with that, and it may be useful for people on here. Feel free to post it as an answer.
Sure thing! I'll do it over this weekend. Actually I might shoot you a few e-mails to make sure i got everything right.
Yeah, perfect! Feel free to use your favorite pet dataset for it too and ask me any questions that come to mind. Cheers!
@Bohdan: Personal email addresses are not used in Biostars posts.
Dear Bohdan Khomtchouk, Hi
Do you know that which one of the Trinity software pipeline can be used directly in MicroScope ?
@Farbod You'll want to look at the Implementation section of the paper to see what your input into MicroScope should be: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1260-x
Hi
The head of "Trinity_Gene_counts_.TMM.EXPR.matrix.csv " is as :
;F1;F2;F3;M1;M2;M3
TRINITY_DN2336_c0_g1;0;0.967;0.209;0;0.201;0.192
TRINITY_DN104307_c0_g1;0.354;0;0;0;1.103;0
TRINITY_DN235187_c0_g1;0;0.34;0;0;0;0
TRINITY_DN151269_c0_g1;0;0.223;0.199;0.754;0.365;0
TRINITY_DN239383_c0_g1;0.26;0.361;0.209;0.142;0.1;0
TRINITY_DN139652_c0_g1;0;0.754;0;0.426;0.155;0.155
can I use this file in microScope ?