Cytofkit

[Lina2016]

A new publication, analysis pipeline similar to what Ted presented at CYTO.

http://journals.plos.org/ploscompbiol/a ... bi.1005112

[mleipold]

Thanks....I'll repost it in Literature

[ErinSimonds]

Cytofkit users -- please upgrade to the latest version to fix a critical bug in the clustering. Users that installed cytofkit via Bioconductor between April 2017 and October 2017 are likely to be affected.

Cross-posted from another thread, posted by the cytofkit dev team earlier today:

Thanks for all the recommendations, and glad to see people using cytofkit!

Unfortunately, a bug was identified regarding how clustering was handled in cytofkit, detailed here.

Thankfully, we've fixed the issue and the fix (along with new features) can be accessed by updating cytofkit.
To do so, you can update your version of R to 3.4.2 and update to Bioconductor v3.6 then run the following:

  Code:

source("https://bioconductor.org/biocLite.R")
biocLite("cytofkit")


- Erin

[ElsaSV]

Hi, I am not able to install Cytofkit in my computer. I am using Mac and R Studio version 3.4.3.

This is the code I am trying to use:

source("https://bioconductor.org/biocLite.R")
biocLite("cytofkit")

library("cytofkit")
cytofkit_GUI()

And this is the error I get:

>library("cytofkit")
Error: package or namespace load failed for ‘cytofkit’:
.onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /opt/X11/lib/libfontconfig.1.dylib
Referenced from: /usr/local/lib/libtk8.6.dylib
Reason: Incompatible library version: libtk8.6.dylib requires version 11.0.0 or later, but libfontconfig.1.dylib provides version 10.0.0
> cytofkit_GUI()
Error in cytofkit_GUI() : could not find function "cytofkit_GUI"

Anyone can help? Thanks!

[markyyy]

Have you followed the complete installation instructions from (I believe) github?

Looks to me like you might not have installed Xcode??

[bc2zbUVA]

Yes, please follow the instructions on the github https://github.com/JinmiaoChenLab/cytofkit.

Also, you may need to install the command line tools and Xquartz. Xcode should come installed on every mac, but you need to explicitly install the command line tools for some R packages. Just search "intstall command line tools xcode [your version of OSx]" and follow the instructions there.

[cytofkitMaintainer]

Yup, Mac has issues that require XQuartz and Xcode,

Here's the steps

Special Notes for Mac Users

For Mac OS X 10.8 or later, you need to install XQuartz to support the GUI:

Download the disk image (dmg) file for XQuartz.

Open the dmg file by double-clicking on it, you'll find XQuartz.pkg, double-click on it to run the installer, clicking through all the defaults.

After the installer runs, you'll have to restart your mac computer.

[nkhanbham]

I have a problem loading the Shniy App (I'm using a PC so not an XQuartz issue). I have installed the packages following the instructions in the Chen paper (though got errors for FNN and digest, so installed these separatrely) loaded libraries, and run the cytofkit GUI. However when the prompt for loading Shiny comes I get stuck with following message

Listening on http://127.0.0.1:4455

Nothing happens after this. Tried aborting and starting again and I always get stuck here. Please help!
Naeem

[nkhanbham]

I have a problem loading the Shiny App (I'm using a PC so not an XQuartz issue). I have installed the packages following the instructions in the Chen paper (though got errors for FNN and digest, so installed these separately), loaded libraries, and run the cytofkit GUI. However when the prompt for loading Shiny comes I get stuck with following message

Listening on http://127.0.0.1:4455

Nothing happens after this. Tried aborting and starting again and I always get stuck here. Please help!
Naeem

[sgranjeaud]

It looks like everything is OK. If you open a Web browser, and write the URL R is listening to, ie http://127.0.0.1:4455, you should get the Shiny interface.
BTW, you should open a new thread instead of replying to this one.