search

GGiecold-zz / ECLAIR

Robust and scalable inference of cell lineages via consensus clustering. Features novel algorithms for the comparison of weighted graphs and unrooted trees.
MIT License
14 stars 4 forks source link

Reproducing Figure 3 and 4 from the original paper #2

Closed falexwolf closed 7 years ago

falexwolf commented 7 years ago

Hi!

I wanted to reproduce Figure 3 and 4 from the Nucleic Acids Research paper but I'm struggling already at finding and providing the data in the correct form.

Is it possible to generate a minimal example where you reproduce these figures and provide the data files or links to the data files?

Thank you, Alex

PS: Actually, I didn't find a single usage example that allows to quickly reproduce a tree from a given dataset.

GGiecold-zz commented 7 years ago

Hi Alex,

After a 2-year stint in computational biology, I have moved on to other endeavors. You should ask Sara Garcia for help. Figures 3 & 4 were added at the request of our reviewer.

Regarding your post-scriptum, the README file in ECLAIR's GitHub repository explains how to automatically process a dataset, and generate those lineage trees. Unfortunately, with endless haggling on how much "technical" information to add to the draft, this was ultimately omitted in the published version of our work.

With kind regards,

Gregory

On Aug 17, 2017 8:46 AM, "Alex Wolf" notifications@github.com wrote:

Hi!

I wanted to reproduce Figure 3 and 4 from the Nucleic Acids Research paper https://doi.org/10.1093/nar/gkw452 but I'm struggling already at finding and providing the data in the correct form.

Is it possible to generate a minimal example where you reproduce these figures and provide the data files or links to the data files?

Thank you, Alex

PS: Actually, I didn't find a single usage example that allows to quickly reproduce a tree from a given dataset.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/GGiecold/ECLAIR/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/AK3j5wzDcRAqmqpplgXlqCCG94srJsi5ks5sZDYQgaJpZM4O6Nhw .

falexwolf commented 7 years ago

Hi Gregory,

thanks for your response! Unfortunately, I can't figure out how to contact Sara; neither your former lab nor another page that google could find list an email address. Do you have it?

Cheers, Alex

GGiecold-zz commented 7 years ago

Hi Alex,

Sara has taken a research staff position at Massachusetts General Hospital. In case they cut off her former account (sgarcia@jimmy.harvard.edu), you can reach her at sara.pinto.garcia@gmail.com or sara_pinto_garcia@hotmail.com

She's been following your work and that of Theis.

With kind regards,

Gregory

On Aug 18, 2017 4:29 AM, "Alex Wolf" notifications@github.com wrote:

Hi Gregory,

thanks for your response! Unfortunately, I can't figure out how to contact Sara; neither your former lab http://bcb.dfci.harvard.edu/%7Egcyuan/people.html nor another page that google could find list an email address. Do you have it?

Cheers, Alex

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/GGiecold/ECLAIR/issues/2#issuecomment-323293656, or mute the thread https://github.com/notifications/unsubscribe-auth/AK3j5_If8QoBO4FJQrrnnHj8CtIzpjRbks5sZUt6gaJpZM4O6Nhw .

falexwolf commented 7 years ago

Thank you! 😄