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Jan 31

cicero batch correct

Hello, I have scATAC time point data (W15 and W19) and want to use Cicero to build trajectory. Here

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cicero batch correct

Hello, I have scATAC time point data (W15 and W19) and want to use Cicero to build trajectory. Here

Jan 31

Shahroze Abbas, hpl...@gmail.com2

9/2/24

Cicero on Very Large Dataset

Apologies for the very late reply. I haven't used CellOracle, but from a quick scan, it seems

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Cicero on Very Large Dataset

Apologies for the very late reply. I haven't used CellOracle, but from a quick scan, it seems

9/2/24

Sophya Yeoh, … hpl...@gmail.com4

11/30/23

Issue with Monocle3 Compatibility

Hello, Looks like you've loaded a monocle object rather than a monocle3 object. Make sure that

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Issue with Monocle3 Compatibility

Hello, Looks like you've loaded a monocle object rather than a monocle3 object. Make sure that

11/30/23

Isaac Diaz, hpl...@gmail.com3

10/26/23

build_gene_activity_matrix error, does chromosome name matter?

Hello, Apologies for the delay. Yes, I think the issue here is going to be the chromosome name. To

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build_gene_activity_matrix error, does chromosome name matter?

Hello, Apologies for the delay. Yes, I think the issue here is going to be the chromosome name. To

10/26/23

Maira Sajjad, hpl...@gmail.com2

3/12/23

issue regarding loading 10x data

Hello, Can you confirm the dimensions of the two objects? Ie provide the head and dims of indata and

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issue regarding loading 10x data

Hello, Can you confirm the dimensions of the two objects? Ie provide the head and dims of indata and

3/12/23

Matt R, hpl...@gmail.com2

12/3/22

Do overlaping groups of cells violate statistical assumptions?

Hi Matt, Yes, the metacells likely share some cells, though in practice the 90% exclusion usually

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Do overlaping groups of cells violate statistical assumptions?

Hi Matt, Yes, the metacells likely share some cells, though in practice the 90% exclusion usually

12/3/22

Stella Kyomen, hpl...@gmail.com2

12/3/22

Error estimating distance parameter value in Cicero

Hi Stella, Sorry for the delay. Can you try setting the max_sample_windows to something larger (1000)

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Error estimating distance parameter value in Cicero

Hi Stella, Sorry for the delay. Can you try setting the max_sample_windows to something larger (1000)

12/3/22

Daniel Gingerich, hpl...@gmail.com2

10/23/22

Multicollinearity in graphical lasso

I'm not sure I entirely understand you question, but yes, the idea with graphical lasso (lasso in

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Multicollinearity in graphical lasso

I'm not sure I entirely understand you question, but yes, the idea with graphical lasso (lasso in

10/23/22

Ben Yang, … hpl...@gmail.com4

4/29/22

Understanding conns data.frame

Thank you for the replies, this makes sense to me! On Sunday, April 17, 2022 at 10:08:52 AM UTC-4 hpl

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Understanding conns data.frame

Thank you for the replies, this makes sense to me! On Sunday, April 17, 2022 at 10:08:52 AM UTC-4 hpl

4/29/22

Pengxin Yang, hpl...@gmail.com2

4/17/22

how to find out the ccan including one peak of my interest

Hi Penny, The CCAN assignments are in the output of the generate_ccans function, so you can just look

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how to find out the ccan including one peak of my interest

Hi Penny, The CCAN assignments are in the output of the generate_ccans function, so you can just look

4/17/22

Daniel Gingerich, hpl...@gmail.com3

4/14/22

smallest number of cells per bin

Hey Hannah, Thanks! That is reassuring to hear, because I had the same thought. I ended up using k =

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smallest number of cells per bin

Hey Hannah, Thanks! That is reassuring to hear, because I had the same thought. I ended up using k =

4/14/22

Daniel Gingerich, hpl...@gmail.com2

4/10/22

cicero with multiple samples

Hi Daniel, I have not tested methods of data integration/batch effect reduction with Cicero before...

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cicero with multiple samples

Hi Daniel, I have not tested methods of data integration/batch effect reduction with Cicero before...

4/10/22

Dongeun Heo, hpl...@gmail.com2

4/10/22

Interpreting Overlap QC metrics

Hi Dongeun, The warning that prints on the vignette is because for the vignette the data size is very

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Interpreting Overlap QC metrics

Hi Dongeun, The warning that prints on the vignette is because for the vignette the data size is very

4/10/22

June Tan, hpl...@gmail.com2

4/10/22

Parameter consideration to increase connection range

Hi Yijun, You'll need to do both. You'll need to increase the window size in order to

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Parameter consideration to increase connection range

Hi Yijun, You'll need to do both. You'll need to increase the window size in order to

4/10/22

chao lu, hpl...@gmail.com2

3/6/22

How to determine “distance” parameters in aggregate_nearby_peaks

Hi Chao, Apologies for the delay. The distance parameter is definitely a bit subjective - you want a

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How to determine “distance” parameters in aggregate_nearby_peaks

Hi Chao, Apologies for the delay. The distance parameter is definitely a bit subjective - you want a

3/6/22

Yura Grabovska, hpl...@gmail.com2

3/6/22

Cicero by cluster as part of Seurat pipeline

Hello, Sorry for the long delay. If I'm understanding correctly, you want to generate a set of

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Cicero by cluster as part of Seurat pipeline

Hello, Sorry for the long delay. If I'm understanding correctly, you want to generate a set of

3/6/22

Yura Grabovska, hpl...@gmail.com3

1/27/22

Two questions: Using Seurat objects as starting point and phastCons

Dear Hannah, Huge apologies about replying almost a year later! I hadn't seen this reply

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Two questions: Using Seurat objects as starting point and phastCons

Dear Hannah, Huge apologies about replying almost a year later! I hadn't seen this reply

1/27/22

Matt R, … Daniel Gingerich3

1/11/22

Comparing two sets of CCANs from different cell type populations

Hi Hannah, I also would like to explore this. I like the bipartite matching concept. I want to merge

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Comparing two sets of CCANs from different cell type populations

Hi Hannah, I also would like to explore this. I like the bipartite matching concept. I want to merge

1/11/22

Daniel Gingerich, hpl...@gmail.com6

10/15/21

Filtering out lowly connected peaks from CCANs

The fisher test did show enrichment of enhancers and promoters in the overall unfiltered CCANs, which

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Filtering out lowly connected peaks from CCANs

The fisher test did show enrichment of enhancers and promoters in the overall unfiltered CCANs, which

10/15/21

Daniel Gingerich, hpl...@gmail.com4

10/15/21

Run cicero on multiple merged cds objects

Hannah, Thanks for the input! I appreciate that you are considering adding that to the next update!

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Run cicero on multiple merged cds objects

Hannah, Thanks for the input! I appreciate that you are considering adding that to the next update!

10/15/21

Matt R, hpl...@gmail.com3

9/2/21

Implementing BigClam in cicero

Hi Hannah! Thanks for getting back to me! I feel your pains with limited bandwidths, but I would like

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Implementing BigClam in cicero

Hi Hannah! Thanks for getting back to me! I feel your pains with limited bandwidths, but I would like

9/2/21

Daniel Gingerich, … hpl...@gmail.com7

9/2/21

cicero inverse correlations

*positive don't outnumber negative* On Thursday, September 2, 2021 at 6:23:01 PM UTC+1 hpl...@

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cicero inverse correlations

*positive don't outnumber negative* On Thursday, September 2, 2021 at 6:23:01 PM UTC+1 hpl...@

9/2/21

nkleine...@gmail.com, hpl...@gmail.com2

9/2/21

Comparing ccans with chIP-seq data.

Hi Niklas, You won't be able to do exactly the same comparison as ChIA-PET because you won't

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Comparing ccans with chIP-seq data.

Hi Niklas, You won't be able to do exactly the same comparison as ChIA-PET because you won't

9/2/21

Daniel Gingerich, hpl...@gmail.com4

8/26/21

Does running cicero on individual chromosomes affect distance parameter?

Thanks Hannah. That makes a lot of sense. In terms of parallel computing I think it would make the

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Does running cicero on individual chromosomes affect distance parameter?

Thanks Hannah. That makes a lot of sense. In terms of parallel computing I think it would make the

8/26/21

Isabelle Lander, hpl...@gmail.com2

8/24/21

Cell aggregation for co-accessibility score calculation

Hi Isabelle, We found in practice that the median number of shared cells was zero even using the

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Cell aggregation for co-accessibility score calculation

Hi Isabelle, We found in practice that the median number of shared cells was zero even using the

8/24/21

chao lu, … Hannah A Pliner9

8/24/21

running error with function “reduceDimension”

Hello, Can you provide the output of traceback() after the error shows up? Sorry for summer slowness,

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running error with function “reduceDimension”

Hello, Can you provide the output of traceback() after the error shows up? Sorry for summer slowness,

8/24/21

Daniel Gingerich

8/14/21

Identifying disease associated CCANs

In WGCNA, the eigengenes of each module are defined as the first principal component of the module.

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Identifying disease associated CCANs

In WGCNA, the eigengenes of each module are defined as the first principal component of the module.

8/14/21

Daniel Gingerich, hpl...@gmail.com2

8/2/21

What is the coaccessibility score

Hi Dan, The coaccessibility score is not quite any of those things... because cicero calculates the

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What is the coaccessibility score

Hi Dan, The coaccessibility score is not quite any of those things... because cicero calculates the

8/2/21

Ciara Mc Mahon, hpl...@gmail.com2

3/25/21

Error at Run Cicero

Hi Ciara, I'm not sure I'll have enough information to help, from what I see in the

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Error at Run Cicero

Hi Ciara, I'm not sure I'll have enough information to help, from what I see in the

3/25/21

chao lu, hpl...@gmail.com4

3/25/21

single-cell accessibility trajectories

Hi, So in that case, there isn't going to be a computational way to determine which gene is being

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single-cell accessibility trajectories

Hi, So in that case, there isn't going to be a computational way to determine which gene is being

3/25/21

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