where to download sciCNV

[NinaJiangL]

hi, I am trying to find the way to download this 'sciCNV' package and use to analysis my single cell data, and I coudnt find a link or source to download it , can you direct me where I can download to perform the scciCNV function with iCNV analysis that you described in method : sciCNV()

Thanks

[NinaJiangL]

and today I had downloaded the "Code" :sciCNV-sciCNV_function zipped file provided on your front page and tried to install three of the files that contained inside the zipped files ( "RTAM Normalization","sciCNV Analysis", "sciCNV_functions") but failed . I am wondering if I need to first install these packages succesfully to R before I can run the function and this can be the interenet failure!

I still could not found the location of all these R script below: source(file.path(path.code, "Mito_umi_gn.R")) source(file.path(path.code, "RTAM_normalization.R")) source(file.path(path.code, "sciCNV.R")) source(file.path(path.code, "Scaling_CNV.R")) source(file.path(path.code, "CNV_score.R")) source(file.path(path.code, "sciCNV.R")) source(file.path(path.code, "Sketch_AveCNV.R")) source(file.path(path.code, "CNV_htmp_glist.R")) source(file.path(path.code, "CNV_htmp_gloc.R")) source(file.path(path.code, "Opt_MeanSD_RTAM1.R")) source(file.path(path.code, "Opt_MeanSD_RTAM2.R")) source(file.path(path.code, "CNV_infer.R"))

The version of my R is 3.5.3 hope someone can answer it, I am really confusing right now. Thanks

[TiedemannLab]

Hi,

thanks for your interest in using our code. I will cc your emails to Ali, whom can try and help you access this.

kind regards, Rodger

Dr. Rodger E. Tiedemann

MB.Ch.B. Ph.D. FRACP FRCPA

Associate Professor of Medicine | UNIVERSITY OF TORONTO

Hematologist & Scientist | PRINCESS MARGARET CANCER CENTRE

Princess Margaret Cancer Research Tower, MaRS

101 College Street, Suite 12-306, Toronto, ON M5G 1L7

Tel: 416-946-2359 | Fax: 416-946-4563

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From: NinaJiangL notifications@github.com Sent: Saturday, January 16, 2021 9:04 AM To: TiedemannLab/sciCNV sciCNV@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [External] [TiedemannLab/sciCNV] where to download sciCNV (#1)

hi, I am trying to find the way to download this 'sciCNV' package and use to analysis my single cell data, and I coudnt find a link or source to download it , can you direct me where I can download to perform the scciCNV function with iCNV analysis that you described in method : sciCNV()

Thanks

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[moutazhelal]

Hi Dr.Tiedemann, I am also interested in using your code. Can you help me?

Thank you very much, Moutaz

[TiedemannLab]

Hi Moutaz,

Thanks for your interest in sciCNV. We’d like to help get you started. I’m cc’ing Ali to address any code-related questions.

Best, Rodger

From: Moutaz Helal notifications@github.com Reply-To: TiedemannLab/sciCNV reply@reply.github.com Date: Thursday, January 28, 2021 at 2:14 PM To: TiedemannLab/sciCNV sciCNV@noreply.github.com Cc: "Tiedemann, Rodger" Rodger.Tiedemann@uhn.ca, Comment comment@noreply.github.com Subject: [External] Re: [TiedemannLab/sciCNV] where to download sciCNV (#1)

Hi Dr.Tiedemann, I am also interested in using your code. Can you help me?

Thank you very much, Moutaz

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[gufranca]

Dear Dr. Tiedemann,

Thank you for providing this amazing tool sciCNV. The heatmaps and the interpretation of the data seems to be the best compared to all the other single-cell CNV inference tools. Like the fellows mentioned in this post, I am also interested in trying out with my scRNA-seq data. How could I install this tool to be able to run the examples? I appreciate any support.

Thank you, Gustavo

[TiedemannLab]

Hi Gustavo

thanks for your comments and email. The code is available on Github and can be run using R. If you have specific questions related to the software side of things, then Ali, my research associate (cc'ed), may be able to assist. Just an FYI that Ali is on vacation at present, so may not be able to answer immediately.

Good luck and please let us know how you get on.

kind regards, Rodger

---

From: gufranca @.> Sent: Friday, April 2, 2021 3:49 PM To: TiedemannLab/sciCNV @.> Cc: Tiedemann, Rodger @.>; Comment @.> Subject: [External] Re: [TiedemannLab/sciCNV] where to download sciCNV (#1)

Dear Dr. Tiedemann,

Thank you for providing this amazing tool sciCNV. The heatmaps and the interpretation of the data seems to be the best compared to all the other single-cell CNV inference tools. Like the fellows mentioned in this post, I am also interested in trying out with my scRNA-seq data. How could I install this tool to be able to run the examples? I appreciate any support.

Thank you, Gustavo

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/TiedemannLab/sciCNV/issues/1*issuecomment-812684507__;Iw!!CjcC7IQ!d3eeoMDQGpilsYp0T-6zlFkKQc79sle-llcGF_5p2Lw46ePXoWA-c2v4bPE4h9jtNOzG$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ANUBYPDERJJU3L7SGU5QYBDTGYNVJANCNFSM4WFJFI2A__;!!CjcC7IQ!d3eeoMDQGpilsYp0T-6zlFkKQc79sle-llcGF_5p2Lw46ePXoWA-c2v4bPE4hzyXHfZy$.

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[Pentayouth]

Dear Dr. Tiedemann,

Thank you and your team for developing the great new tool for scCNV detection. However, there are too many mistakes mixing up with redundant codes, which makes the scripts really hard to read and follow. Please consider checking the code to ensure the vignette could be executed properly.

Best regards, Pentayouth

[TiedemannLab]

Hi Pentayouth,

thanks for your suggestion, which I'll pass on to my research associate, Ali, whom was responsible for the coding of the method. I do hope that we can streamline this for wider use. At present Ali is on a short a vacation, but I'll ask him to have a look at this on his return.

kind regards,

Rodger

---

From: Pentayouth @.> Sent: Tuesday, April 6, 2021 10:58 AM To: TiedemannLab/sciCNV @.> Cc: Tiedemann, Rodger @.>; Comment @.> Subject: [External] Re: [TiedemannLab/sciCNV] where to download sciCNV (#1)

Dear Dr. Tiedemann,

Thank you and your team for developing the great new tool for scCNV detection. However, there are too many mistakes mixing up with redundant codes, which makes the scripts really hard to read and follow. Please consider checking the code to ensure the vignette could be executed properly thoroughly.

Best regards, Pentayouth

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/TiedemannLab/sciCNV/issues/1*issuecomment-814189629__;Iw!!CjcC7IQ!cmAtKzkc8tBL_7BPUxwV3pWJ13lRoEr2MU8h39M54xZsu2qCRYgdNopsY6RZzAAe0Iot$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ANUBYPDMRWQDPR3N7MYRH53THMOP7ANCNFSM4WFJFI2A__;!!CjcC7IQ!cmAtKzkc8tBL_7BPUxwV3pWJ13lRoEr2MU8h39M54xZsu2qCRYgdNopsY6RZzIbNxK-e$.

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[gufranca]

Thanks Dr. Tiedemann. I agree with Pentayouth that if Ali would be able to make this great tool more user friendly as an installable package with all the dependencies will be of great value to the community. Looking forward to be able to use it! Gustavo

[MelissaSaichi]

Dear Dr.Tiedemann, I am also willing to test this tool which seems to give better representations and easier interpretations. How could I install the tool and start using it ? Many thanks for your help, Melissa