Can this tool be used for spatial transcriptome data?

[xxbb23]

Hi CytoSig developers:

Thank you very much for your amazing tool!
I am currently analyzing spatial transcriptomics data and need to investigate the activity of a specific inflammatory factor within a particular region. Therefore, can Cytosig be used for spatial transcriptomics data analysis?
Thank you!

[data2intelligence]

Hi, xxbb23, Yes, you can summarize the spatial transcriptomics (ST) data as an input matrix to CytoSig. Then, you will get the output for each ST spot. Sincerely, Peng On Sep 21, 2025, at 1:46 AM, X-Chen ***@***.***> wrote:  [https://avatars.githubusercontent.com/u/99854587?s=20&v=4]xxbb23 created an issue (data2intelligence/CytoSig#20)<#20> Hi CytoSig developers: Thank you very much for your amazing tool! I am currently analyzing spatial transcriptomics data and need to investigate the activity of a specific inflammatory factor within a particular region. Therefore, can Cytosig be used for spatial transcriptomics data analysis? Thank you! — Reply to this email directly, view it on GitHub<#20>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AQRREFYUUTOJ7WPQP6ESSCT3TY3RVAVCNFSM6AAAAACHCKIRY6VHI2DSMVQWIX3LMV43ASLTON2WKOZTGQZTOOBUG44DEOI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

[beibeiru]

Hi,

We have developed a new software tool, SecAct, to estimate the activity of over 1,000 secreted proteins in spatial transcriptomics data.
~ Tutorial for Visium: https://data2intelligence.github.io/SecAct/articles/stPattern.html.
~ Tutorial for CosMx: https://data2intelligence.github.io/SecAct/articles/stCCC.html.

SecAct uses newly generated signatures. If you would like to use the previous signatures from CytoSig instead, please follow the settings below.

SpaCET_obj <- SecAct.activity.inference.ST(
  inputProfile = SpaCET_obj,
  sigMatrix = "CytoSig",
  is.group.sig = TRUE,
  scale.factor = 10000
)

Best,
Beibei

[xxbb23]

Thanks!

…

---- Replied Message ---- | From | Beibei ***@***.***> | | Date | 02/21/2026 03:59 | | To | ***@***.***> | | Cc | ***@***.***>***@***.***> | | Subject | Re: [data2intelligence/CytoSig] Can this tool be used for spatial transcriptome data? (Issue #20) | beibeiru left a comment (data2intelligence/CytoSig#20) Hi, We have developed a new software tool, SecAct, to estimate the activity of over 1,000 secreted proteins in spatial transcriptomics data. ~ Tutorial for Visium: https://data2intelligence.github.io/SecAct/articles/stPattern.html. ~ Tutorial for CosMx: https://data2intelligence.github.io/SecAct/articles/stCCC.html. SecAct uses newly generated signatures. If you would like to use the previous signatures from CytoSig instead, please follow the settings below. SpaCET_obj<- SecAct.activity.inference.ST( inputProfile=SpaCET_obj, sigMatrix="CytoSig", is.group.sig=TRUE, scale.factor=10000 ) Best, Beibei — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>