canopy_phylogeny

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Hi everyone!

Thanks for your interest in Canopy! Here is the official Q&A forum for the R package Canopy. If you've any questions regarding the software, please don't hesitate posting them here. You can also email us at canopy_phylogeny@googlegroups.com. We will try our best to reply ASAP.

Cheers,

Yuchao

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9/14/23

Questions about generate WM by processed data

Hi Yuchao, I am interested in using the Canopy method to construct a phylogenetic tree using publicly

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Questions about generate WM by processed data

Hi Yuchao, I am interested in using the Canopy method to construct a phylogenetic tree using publicly

9/14/23

5/13/21

Question about the C Matrix

Hello Yuchao Jiang, I hope you are alright and safe, I am using Canopy in my master's

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Question about the C Matrix

Hello Yuchao Jiang, I hope you are alright and safe, I am using Canopy in my master's

5/13/21

4/16/21

Re: tumor purity estimation by Canopy

Hi Jinxiong, Thanks for your interest in Canopy. The tumor purity is 1-the percentage of normal cells

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Re: tumor purity estimation by Canopy

Hi Jinxiong, Thanks for your interest in Canopy. The tumor purity is 1-the percentage of normal cells

4/16/21

4/9/20

Re: Sequenza demo

Dear Sabra, For our own analysis, we always uses FALCON-X and don't have a readily available

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Re: Sequenza demo

Dear Sabra, For our own analysis, we always uses FALCON-X and don't have a readily available

4/9/20

yuliu...@gmail.com

3/31/20

input of canopy

Hi, I'd like to use Canopy for my work. But I only have results from WES for tumor. There is no

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input of canopy

Hi, I'd like to use Canopy for my work. But I only have results from WES for tumor. There is no

3/31/20

3/17/20

Re: Code for simulation experiment in Canopy paper

Hi, Thanks for your interest. This work was published in 2016 and the simulation was performed a year

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Re: Code for simulation experiment in Canopy paper

Hi, Thanks for your interest. This work was published in 2016 and the simulation was performed a year

3/17/20

Jiang, Yuchao, Bonneville, Russell4

11/7/19

RE: Canopy estimation of normal contamination

Hello Dr. Jiang, Thank you very much for your suggestions and insights! With our -20% normal floor,

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RE: Canopy estimation of normal contamination

Hello Dr. Jiang, Thank you very much for your suggestions and insights! With our -20% normal floor,

11/7/19

Wandinger, Caroline Sophie, Jiang, Yuchao2

10/15/19

config.summary of Canopy

Hi Caroline, Thanks for your interests in Canopy and your insightful questions. See below for my

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config.summary of Canopy

Hi Caroline, Thanks for your interests in Canopy and your insightful questions. See below for my

10/15/19

iams...@gmail.com

5/23/19

Single-sample performance

Hello, Apologies if this has been asked before, but have you explored the performance of Canopy using

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Single-sample performance

Hello, Apologies if this has been asked before, but have you explored the performance of Canopy using

5/23/19

Simon, Yuchao Jiang3

3/13/19

From FALCON to Canopy with multiple samples

Hi Simon, Thanks for your interest in Canopy. For your first question, there's no currently no

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From FALCON to Canopy with multiple samples

Hi Simon, Thanks for your interest in Canopy. For your first question, there's no currently no

3/13/19

Liu, Delong (NIH/NHLBI) [E], … Yuchao Jiang7

12/6/18

question about canopy.post()

On Nov 16, 2018, at 12:22 AM, ame...@b612.email wrote: Hi Yuchao, Thanks for your quick reply. I want

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question about canopy.post()

On Nov 16, 2018, at 12:22 AM, ame...@b612.email wrote: Hi Yuchao, Thanks for your quick reply. I want

12/6/18

ame...@b612.email, Yuchao Jiang4

12/6/18

Questions about WM regions on mutiplesamples

This example is just for illustration and we have not implemented the auto-parsing and auto-curation

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Questions about WM regions on mutiplesamples

This example is just for illustration and we have not implemented the auto-parsing and auto-curation

12/6/18

12/6/18

Re: SEG file for Canopy?

Hi Chunyang, Thanks for your interest in Canopy and truly sorry for my late reply. We've

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Re: SEG file for Canopy?

Hi Chunyang, Thanks for your interest in Canopy and truly sorry for my late reply. We've

12/6/18

ame...@b612.email, Yuchao Jiang2

12/6/18

questioa bout burnin and thin

If you are not sure which values to set or don't understand what burnin and thinning mean, I

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questioa bout burnin and thin

If you are not sure which values to set or don't understand what burnin and thinning mean, I

12/6/18

Vince R, … Yuchao Jiang4

11/20/18

Selection of variants and CN

This has been clearly stated in the user manual. I recommend go through it thoroughly. On Tue, Nov 20

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Selection of variants and CN

This has been clearly stated in the user manual. I recommend go through it thoroughly. On Tue, Nov 20

11/20/18

Linda Sundermann, … Yuchao Jiang9

9/11/18

Unexplained Errors

Hi Yuchao, thanks for adding this and thank for suggesting alternative methods. Best regards, Linda

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Unexplained Errors

Hi Yuchao, thanks for adding this and thank for suggesting alternative methods. Best regards, Linda

9/11/18

Jiang, Yuchao, … Yuchao Jiang11

8/3/18

Re: Running CODEX2 Somatic WES

Hi Brad, In this case, I am not sure either. Do you have positive or negative controls for you to

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Re: Running CODEX2 Somatic WES

Hi Brad, In this case, I am not sure either. Do you have positive or negative controls for you to

8/3/18

achao...@gmail.com, Gene Urrutia12

7/26/18

canopy.sample.parallel

Hi Peter, The total read depth should be calculated from the sequencing alignments. We recommend

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canopy.sample.parallel

Hi Peter, The total read depth should be calculated from the sequencing alignments. We recommend

7/26/18

Gene Urrutia, … Jiang, Yuchao3

6/14/18

Re: MARATHON pipeline

Hi Oliver, FALCON takes as input allele-specific read counts at germline heterozygous loci and

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Re: MARATHON pipeline

Hi Oliver, FALCON takes as input allele-specific read counts at germline heterozygous loci and

6/14/18

Jiang, Yuchao, … Gene Urrutia6

4/25/18

Re: multiple overlap regions in canopy

Hi Lorraine, Thanks again for your interest in Canopy and the Marathon pipeline. Yes you are correct,

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Re: multiple overlap regions in canopy

Hi Lorraine, Thanks again for your interest in Canopy and the Marathon pipeline. Yes you are correct,

4/25/18

Jiang, Yuchao, … Gene Urrutia3

4/25/18

RE: [yuchaojiang/Canopy] Clustering with 1 Sample (#8)

Hi Lorraine, Thank you for your interest in Canopy and the Marathon pipeline. I would suggest

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RE: [yuchaojiang/Canopy] Clustering with 1 Sample (#8)

Hi Lorraine, Thank you for your interest in Canopy and the Marathon pipeline. I would suggest

4/25/18

Lara Luis, … Yuchao Jiang4

4/10/18

Running Canopy on Amplicon Sequencing

Thanks Gene and Yuchao, very informative reply. Cheers, Luis ________________________________________

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Running Canopy on Amplicon Sequencing

Thanks Gene and Yuchao, very informative reply. Cheers, Luis ________________________________________

4/10/18

Urrutia, Eugene

4/9/18

Question about getting WM and Wm

Hi Lorraine, Thank you for your interest in Canopy and the MARATHON pipeline. please see our function

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Question about getting WM and Wm

Hi Lorraine, Thank you for your interest in Canopy and the MARATHON pipeline. please see our function

4/9/18

Jiang, Yuchao, Linda Sundermann2

1/29/18

Re: Problems with Canopy

Thank you, Yuchao! I will try this. Best regards, Linda Am 1/28/18 um 8:07 AM schrieb Jiang, Yuchao:

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Re: Problems with Canopy

Thank you, Yuchao! I will try this. Best regards, Linda Am 1/28/18 um 8:07 AM schrieb Jiang, Yuchao:

1/29/18

Jia, Li (NIH/NCI) [C], … Yuchao Jiang8

1/28/18

Questions on Canopy package

On Jan 26, 2018, at 10:06 AM, Jia, Li (NIH/NCI) [C] <li....@nih.gov> wrote: Thanks Yuchao for

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Questions on Canopy package

On Jan 26, 2018, at 10:06 AM, Jia, Li (NIH/NCI) [C] <li....@nih.gov> wrote: Thanks Yuchao for

1/28/18

ljia...@gmail.com, Yuchao Jiang2

1/16/18

question on canopy.output error

Hi Emily, Something is wrong. Can you send the image file (use save.image() function) and we will

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question on canopy.output error

Hi Emily, Something is wrong. Can you send the image file (use save.image() function) and we will

1/16/18

1/4/18

Re: running MARATHON and Canopy, starting from VCF and BAM files

Hi Joern, Thanks for your interest in MARATHON and Canopy. In short to your answer, here you can find

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Re: running MARATHON and Canopy, starting from VCF and BAM files

Hi Joern, Thanks for your interest in MARATHON and Canopy. In short to your answer, here you can find

1/4/18

Chen, Hui-Zi, … Roychowdhury, Sameek3

12/22/17

RE: Inquiries into software Canopy

Thanks very much for your time and feedback! Sameek From: Jiang, Yuchao [mailto:yuc...@email.unc.edu

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RE: Inquiries into software Canopy

Thanks very much for your time and feedback! Sameek From: Jiang, Yuchao [mailto:yuc...@email.unc.edu

12/22/17

11/22/17

Re: Correspondence: Some important questions regarding CANOPY

I think I've replied most of your questions, via a different thread. See below again. Yuchao On

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Re: Correspondence: Some important questions regarding CANOPY

I think I've replied most of your questions, via a different thread. See below again. Yuchao On

11/22/17

Jiang, Yuchao, Yuchao Jiang2

11/17/17

Re: Integrative pipeline for profiling DNA copy,number and inferring tumor phylogeny and Canopy

https://github.com/yuchaojiang/Canopy See under “Common questions” for more details. On Nov 17, 2017,

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Re: Integrative pipeline for profiling DNA copy,number and inferring tumor phylogeny and Canopy

https://github.com/yuchaojiang/Canopy See under “Common questions” for more details. On Nov 17, 2017,

11/17/17

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