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Danko-Lab / BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
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Differential Expression and GSEA #51

Open emilylasse opened 1 year ago

emilylasse commented 1 year ago

Would you be able to provide your code for how to performed different gene expression and GSEA? Ultimately, I'm looking to make a plot like Figure 3D from your paper. Thanks

tinyi commented 1 year ago

yes. I will upload it shortly.

On Wed, Jul 19, 2023 at 3:55 PM emilylasse @.***> wrote:

Would you be able to provide your code for how to performed different gene expression and GSEA? Ultimately, I'm looking to make a plot like Figure 3D from your paper. Thanks

— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/BayesPrism/issues/51, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHS2FETAXUJZIGOCP7ITXRA3RZANCNFSM6AAAAAA2QNAJKM . You are receiving this because you are subscribed to this thread.Message ID: @.***>

tinyi commented 1 year ago

Hi Emily,

Sorry for the delay. I have jsut uploaded the scripts to https://github.com/tinyi/BayesPrism_downstream_analysis/tree/main/Figure_3d , along with the input and output required for running the script. You may need to install pdfjam for plotting the concatenated version. If not, we can generate individual plots by modifying the corresponding lines.

Best,

Tinyi

On Thu, Jul 20, 2023 at 1:31 PM Tinyi Chu @.***> wrote:

yes. I will upload it shortly.

On Wed, Jul 19, 2023 at 3:55 PM emilylasse @.***> wrote:

Would you be able to provide your code for how to performed different gene expression and GSEA? Ultimately, I'm looking to make a plot like Figure 3D from your paper. Thanks

— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/BayesPrism/issues/51, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHS2FETAXUJZIGOCP7ITXRA3RZANCNFSM6AAAAAA2QNAJKM . You are receiving this because you are subscribed to this thread.Message ID: @.***>

emilylasse commented 1 year ago

Thank you for the code

Emily

On Fri, Jul 28, 2023 at 7:14 PM Tinyi Chu @.***> wrote:

Hi Emily,

Sorry for the delay. I have jsut uploaded the scripts to https://github.com/tinyi/BayesPrism_downstream_analysis/tree/main/Figure_3d , along with the input and output required for running the script. You may need to install pdfjam for plotting the concatenated version. If not, we can generate individual plots by modifying the corresponding lines.

Best,

Tinyi

On Thu, Jul 20, 2023 at 1:31 PM Tinyi Chu @.***> wrote:

yes. I will upload it shortly.

On Wed, Jul 19, 2023 at 3:55 PM emilylasse @.***> wrote:

Would you be able to provide your code for how to performed different gene expression and GSEA? Ultimately, I'm looking to make a plot like Figure 3D from your paper. Thanks

— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/BayesPrism/issues/51, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AB4NHS2FETAXUJZIGOCP7ITXRA3RZANCNFSM6AAAAAA2QNAJKM>

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/BayesPrism/issues/51#issuecomment-1656429899, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBA3KEZ7RQXACDQGZ4IZVL3XSRBW5ANCNFSM6AAAAAA2QNAJKM . You are receiving this because you authored the thread.Message ID: @.***>