Puram et.al Source code

[smk5g5]

Hi,

I was wondering how I can gain access to the code used in Puram et.al paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5878932/). The paper talks about software being available in https://github.com/NCIP/Trinity_CTAT/wiki but all I see is the wiki. How do I get my hands on the source code kindly help?

Best!

[brianjohnhaas]

Hi,

I expect they were making reference to this: https://github.com/broadinstitute/inferCNV/wiki

which is part of the Trinity CTAT software ecosystem.

best,

~b

On Wed, Jan 15, 2020 at 2:16 AM Saad khan notifications@github.com wrote:

Hi,

I was wondering how I can gain access to the code used in Puram et.al paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5878932/). The paper talks about software being available in https://github.com/NCIP/Trinity_CTAT/wiki but all I see is the wiki. How do I get my hands on the source code kindly help?

Best!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/NCIP/Trinity_CTAT/issues/4?email_source=notifications&email_token=ABZRKX3ZLK5BW4FY6DH52OLQ5ZPXBA5CNFSM4KG4CPT2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IGG6J5Q, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX4H4QI43HQAEIOMZU3Q5ZPXBANCNFSM4KG4CPTQ .

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[smk5g5]

I think the paper talks about some matlab scripts being available at this link.

MATLAB scripts for analyses	Trinity Cancer Transcriptome Analysis Toolkit	https://github.com/NCIP/Trinity_CTAT/wiki

I am particularly interested in "Inferring Cancer-cell Specific Expression" section and if there is a code available for that somewhere in the trinity toolkit.

Thanks!

[brianjohnhaas]

I'm not sure about any matlab code... Our implementation is in R and available through bioconductor.

Try writing the original authors for more clarity on this and anything you're after that's not provided as part of the infercnv software.

best,

~b

On Wed, Jan 15, 2020 at 10:05 AM Saad khan notifications@github.com wrote:

I think the paper talks about some matlab scripts being available at this link. MATLAB scripts for analyses Trinity Cancer Transcriptome Analysis Toolkit https://github.com/NCIP/Trinity_CTAT/wiki

I am particularly interested in "Inferring Cancer-cell Specific Expression" section and if there is a code available for that somewhere in the trinity toolkit.

Thanks!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/NCIP/Trinity_CTAT/issues/4?email_source=notifications&email_token=ABZRKX6XDGWXVI2LGFMDSTDQ54Q5JA5CNFSM4KG4CPT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJAT2MY#issuecomment-574700851, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX4HJTKSKUGPQHZCIATQ54Q5JANCNFSM4KG4CPTQ .

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

[zym826]

Hello, I would like to know where can I find the R source code of this article called Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

[brianjohnhaas]

Hi,

Please contact the corresponding author for the manuscript. We don't have anything available as part of the infercnv project itself for it.

On Mon, Jul 5, 2021 at 10:10 PM zym826 @.***> wrote:

Hello, I would like to know where can I find the R source code of this article called Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/NCIP/Trinity_CTAT/issues/4#issuecomment-874409195, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX6DZTVX7XN3HW4Z43LTWJQ2DANCNFSM4KG4CPTQ .

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas