Develop LACE-view: a visualizer for Longitudinal Clonal Trees

marcoxa commented 4 years ago

Background

The BIMIB/DCB group at the Universita` degli Studi di Milano-Bicocca has constructed a series of algorithms and tools to study the Cancer Evolution from Single Cells in the context of the Accelerator Award Project "Single-Cells Cancer Evolution in the Clinic". The tool, called LACE, is the result of several previous developments in the study of "Reconstruction of Cancer Progression" (CAPRESE, CAPRI, TRAIT, TRONCO). Once a mutational matrix is generated from Single-Cells (SCs) data (e.g., RNA-seq transcriptomic measures), organized in "time-points", LACE can reconstruct a "clonal history" of a tumor. The obvious application being the study of the effect of therapy administration.

Goal

At the time of this writing, LACE, a R application, produces a set of numeric results that can be used to produce Timescape fish-plots describing the clonal histories supported by data. The same results can be used to produce "longitunal clonal trees" that convey information about the actual distribution of clones (i.e, the single cells) over time.

The goal of the LACE-view project will be to provide a visualization tool for longitudinal clonal histories and trees (therefore usable also for other tools in the TRONCO suite) to be used by a biologist/bioinformatician to explore th implications of an analysis run with LACE, such as clonal expansion, shrinking, emergence and extinction.

The architecture of the tool will be based on a REST API that will connect the LACE tool to a cytoscape.js web based visualization, or to a Jupyter special visualization cell. Of course, every item in the clonal history display will have to be connected to the raw SCs data and to the ancillary information retrievable from various available databases.

Difficulty level: 2

Prior experience with cytoscape.js app development or extensive Javascript experience highly recommended. R (and Python) also useful as well as knowledge of SBGN as a possible exchange format.

Skills

R, Cytoscape.js, cyREST, Javascript, Node.js.

Repository

TBA

References

Ramazzotti, D. et al, Longitudinal Cancer Evolution from Single Cells, https://www.biorxiv.org/content/10.1101/2020.01.14.906453v1

Potential Mentors

Marco Antoniotti Alex Graudenzi Daniele Ramazzotti

Contact

Marco Antoniotti (mailto:marco.antoniotti@unimib.it)

sauravhiremath commented 4 years ago

This issue suits my interest and strengths. I have extensive experience with Javascript, NodeJS and Deep Learning. I'm also a Bioinformatics student, so have good knowledge about the internal working. May I know how could I proceed further in this project? @marcoxa

EDIT: Sorry I don't know who exactly to tag @alexgraudenzi @danro9685 . Would be great if anyone of you could help me out

marcoxa commented 4 years ago

Dear sauravhiremat

glad to hear that this project may interest you. Tagging me and the other guys is ok. We all talk.

If this interests you you should go ahead and formulate a project, ideally for a web based tool to eventually submit it to NRNB. We can discuss the details beforehand.

Were are you located?

All the best

Marco

sauravhiremath commented 4 years ago

I'm from Vellore Institute of Technology, Vellore, India.

Yeah I would further like to discuss upon the proposal

On Fri, 13 Mar, 2020, 6:17 pm Marco Antoniotti, notifications@github.com wrote:

Dear sauravhiremat

glad to hear that this project may interest you. Tagging me and the other guys is ok. We all talk.

If this interests you you should go ahead and formulate a project, ideally for a web based tool to eventually submit it to NRNB. We can discuss the details beforehand.

Were are you located?

All the best

Marco

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/147#issuecomment-598703298, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG2QVWZO6G5XMLMCYKIM2STRHITPHANCNFSM4KLWVPGA .

bhaveshnarra commented 4 years ago

Hi @marcoxa , @alexgraudenzi , @danro9685 I am bhavesh a final year undergrad student from BITS Pilani India. I really like the project and would be submitting a proposal. I have contributed here before as a GSOC 2017 student and I am really pumped to be contributing again.

bhaveshnarra commented 4 years ago

Hi @marcoxa , @alexgraudenzi , @danro9685 I want to make a demo for my proposal showcasing a web application that calls the LACE backend hosted on a server and displays it using cytsoscape.js. I was successful in running LACE locally but I have a problem interpreting the results. I ran their example as stated but I wasn't able to understand the result. I will post the output here for reference. Thanks in advance.

bhaveshnarra commented 4 years ago

print(inference) $B Root ARPC2_2_218249894_C_T PRAME_22_22551005_T_A HNRNPC_14_21211843_C_T Root 1 0 0 0 Clone_1 1 1 0 0 Clone_2 1 1 1 0 Clone_3 1 1 1 1 Clone_4 1 1 1 0 Clone_5 1 1 0 0 Clone_6 1 1 1 0 COL1A2_7_94422978_C_A RPL5_1_92837514_C_G CCT8_21_29063389_G_A Root 0 0 0 Clone_1 0 0 0 Clone_2 0 0 0 Clone_3 0 0 0 Clone_4 1 0 0 Clone_5 0 1 0 Clone_6 1 0 1

$C $C$Experiment_1 Clone SRR7424153 3 SRR7424154 4 SRR7424155 2 SRR7424156 1 SRR7424159 6 SRR7424160 4 SRR7424161 6 SRR7424162 4 SRR7424163 6 SRR7424164 6 SRR7424165 4 SRR7424166 4 SRR7424167 2 SRR7424168 2 SRR7424170 4 SRR7424172 1 SRR7424173 3 SRR7424174 4 SRR7424175 5 SRR7424176 4 SRR7424177 2 SRR7424178 1 SRR7424179 1 SRR7424180 2 SRR7424181 4 SRR7424182 1 SRR7424183 4 SRR7424184 6 SRR7424185 4 SRR7424186 5 SRR7424187 4 SRR7424188 1 SRR7424190 1 SRR7424191 4 SRR7424192 4 SRR7424193 1 SRR7424194 4 SRR7424195 6 SRR7424196 2 SRR7424197 4 SRR7424198 4 SRR7424199 6 SRR7424200 4 SRR7424201 1 SRR7424203 2 SRR7424204 6 SRR7424205 4 SRR7424206 2 SRR7424207 5 SRR7424208 2 SRR7424210 1 SRR7424211 2 SRR7424212 2 SRR7424213 6 SRR7424214 6 SRR7424215 3 SRR7424216 1 SRR7424217 4 SRR7424218 6 SRR7424219 4 SRR7424220 1 SRR7424221 4 SRR7424222 6 SRR7424223 1 SRR7424224 2 SRR7424226 4 SRR7424227 5 SRR7424228 2 SRR7424229 6 SRR7424230 4 SRR7424232 6 SRR7424233 4 SRR7424234 2 SRR7424235 2 SRR7424237 6 SRR7424238 6 SRR7424239 2 SRR7424240 4 SRR7424241 4 SRR7424242 4 SRR7424243 1 SRR7424244 2 SRR7424245 4 SRR7424246 1 SRR7424247 2 SRR7424248 5 SRR7424249 2 SRR7424251 1 SRR7424252 3 SRR7424255 5 SRR7424257 1 SRR7424258 5 SRR7424259 5 SRR7424260 3 SRR7424261 4 SRR7424262 1 SRR7424265 6 SRR7424266 3 SRR7424267 4 SRR7424268 6 SRR7424269 1 SRR7424270 3 SRR7424271 1 SRR7424272 1 SRR7424273 4 SRR7424274 3 SRR7424275 2 SRR7424277 2 SRR7424278 6 SRR7424279 1 SRR7424280 3 SRR7424281 1 SRR7424282 4 SRR7424284 5 SRR7424285 1 SRR7424286 3 SRR7424287 4 SRR7424288 1 SRR7424289 6 SRR7424290 5 SRR7424292 1 SRR7424293 4 SRR7424294 2 SRR7424295 2 SRR7424296 4 SRR7424297 4 SRR7424298 5 SRR7424300 4 SRR7424302 1 SRR7424303 6 SRR7424304 5 SRR7424305 6 SRR7424306 2 SRR7424307 6 SRR7424308 5 SRR7424309 1 SRR7424310 4 SRR7424311 5 SRR7424312 3 SRR7424313 2 SRR7424314 2 SRR7424318 1 SRR7424319 4 SRR7424320 5 SRR7424321 4 SRR7424322 6

$C$Experiment_2 Clone SRR7424324 6 SRR7424325 6 SRR7424326 4 SRR7424327 4 SRR7424328 6 SRR7424329 6 SRR7424330 4 SRR7424331 3 SRR7424332 6 SRR7424333 6 SRR7424335 1 SRR7424336 6 SRR7424337 2 SRR7424339 2 SRR7424340 1 SRR7424341 1 SRR7424342 3 SRR7424344 1 SRR7424345 4 SRR7424346 4 SRR7424347 1 SRR7424348 2 SRR7424349 2 SRR7424350 2 SRR7424352 4 SRR7424353 2 SRR7424354 2 SRR7424355 1 SRR7424356 1 SRR7424357 4 SRR7424358 1 SRR7424359 6 SRR7424360 4 SRR7424361 1 SRR7424363 6 SRR7424364 2 SRR7424365 4 SRR7424366 2 SRR7424367 4 SRR7424368 3 SRR7424369 3 SRR7424370 2 SRR7424371 1 SRR7424372 3 SRR7424375 4 SRR7424376 6 SRR7424379 2 SRR7424381 6 SRR7424382 2 SRR7424385 3 SRR7424386 3 SRR7424387 2 SRR7424388 6 SRR7424389 6 SRR7424390 1 SRR7424391 2 SRR7424395 1 SRR7424396 2 SRR7424397 4 SRR7424398 2 SRR7424399 1 SRR7424400 2 SRR7424401 4 SRR7424402 4 SRR7424403 1 SRR7424404 2 SRR7424405 1 SRR7424406 4 SRR7424407 4 SRR7424408 1 SRR7424409 6 SRR7424411 6 SRR7424412 4 SRR7424413 4 SRR7424416 2 SRR7424417 1 SRR7424419 2 SRR7424420 3 SRR7424423 4 SRR7424424 4 SRR7424425 3 SRR7424426 4 SRR7424430 1 SRR7424431 2 SRR7424434 2 SRR7424435 2 SRR7424437 3 SRR7424438 2 SRR7424441 1 SRR7424442 1 SRR7424444 1 SRR7424445 6 SRR7424450 1 SRR7424451 1 SRR7424452 2 SRR7424453 4 SRR7424454 2 SRR7424455 1 SRR7424457 1 SRR7424460 1 SRR7424463 2 SRR7424464 2 SRR7424465 6 SRR7424466 2 SRR7424468 3 SRR7424470 1 SRR7424471 6 SRR7424472 2 SRR7424473 3 SRR7424475 1 SRR7424476 1

$C$Experiment_3 Clone SRR7424479 3 SRR7424480 4 SRR7424482 4 SRR7424484 4 SRR7424485 4 SRR7424486 1 SRR7424487 1 SRR7424488 4 SRR7424489 6 SRR7424491 6 SRR7424493 4 SRR7424494 1 SRR7424497 1 SRR7424498 4 SRR7424499 4 SRR7424505 2 SRR7424506 3 SRR7424507 2 SRR7424509 1 SRR7424512 2 SRR7424515 1 SRR7424517 1 SRR7424518 2 SRR7424523 2 SRR7424524 2 SRR7424528 6 SRR7424529 2 SRR7424530 3 SRR7424532 4 SRR7424538 1 SRR7424543 1 SRR7424544 4 SRR7424545 2 SRR7424546 1 SRR7424554 6 SRR7424561 2 SRR7424565 2 SRR7424566 1 SRR7424567 1 SRR7424569 6 SRR7424571 2 SRR7424577 4 SRR7424579 6 SRR7424580 6 SRR7424583 2 SRR7424584 6 SRR7424585 2 SRR7424586 1 SRR7424587 6 SRR7424591 4 SRR7424592 1 SRR7424593 2 SRR7424595 4 SRR7424596 4 SRR7424597 4 SRR7424598 1 SRR7424600 6 SRR7424603 1 SRR7424605 1 SRR7424607 1 SRR7424608 6 SRR7424611 4 SRR7424614 6 SRR7424616 1 SRR7424618 2 SRR7424619 4 SRR7424620 3 SRR7424624 1 SRR7424628 6 SRR7424630 1 SRR7424631 4 SRR7424632 1 SRR7424634 6 SRR7424636 2 SRR7424638 1 SRR7424642 4 SRR7424645 3 SRR7424646 6 SRR7424647 4 SRR7424648 1 SRR7424649 6 SRR7424653 6 SRR7424656 1 SRR7424660 6 SRR7424662 4 SRR7424664 6 SRR7424665 6 SRR7424666 1 SRR7424671 2 SRR7424673 4

$C$Experiment_4 Clone SRR7424678 1 SRR7424680 6 SRR7424681 2 SRR7424682 4 SRR7424684 1 SRR7424685 1 SRR7424686 2 SRR7424687 1 SRR7424688 4 SRR7424689 1 SRR7424691 4 SRR7424692 4 SRR7424693 3 SRR7424694 1 SRR7424695 1 SRR7424696 6 SRR7424697 6 SRR7424698 3 SRR7424699 6 SRR7424700 3 SRR7424701 5 SRR7424702 2 SRR7424703 1 SRR7424705 6 SRR7424706 2 SRR7424707 6 SRR7424708 6 SRR7424709 2 SRR7424710 1 SRR7424711 2 SRR7424712 2 SRR7424713 3 SRR7424714 1 SRR7424715 2 SRR7424716 1 SRR7424717 1 SRR7424719 3 SRR7424721 1 SRR7424722 1 SRR7424723 2 SRR7424724 4 SRR7424725 5 SRR7424726 2 SRR7424727 1 SRR7424728 2 SRR7424729 1 SRR7424730 4 SRR7424731 2 SRR7424732 5 SRR7424733 6 SRR7424734 3 SRR7424735 1 SRR7424736 1 SRR7424737 2 SRR7424738 2 SRR7424739 2 SRR7424740 1 SRR7424741 2 SRR7424742 5 SRR7424743 2 SRR7424744 3 SRR7424745 6 SRR7424746 1 SRR7424747 6 SRR7424748 2 SRR7424749 1 SRR7424750 5 SRR7424751 6 SRR7424753 5 SRR7424754 5 SRR7424755 5 SRR7424756 2 SRR7424757 5 SRR7424758 1 SRR7424759 5 SRR7424760 2 SRR7424761 5 SRR7424762 1 SRR7424763 2 SRR7424764 5 SRR7424765 5 SRR7424766 3 SRR7424768 3 SRR7424769 1 SRR7424770 6 SRR7424772 5 SRR7424774 6 SRR7424775 6 SRR7424778 2 SRR7424779 5 SRR7424780 5 SRR7424781 3 SRR7424784 2 SRR7424785 2 SRR7424786 1 SRR7424787 3 SRR7424788 1 SRR7424789 2 SRR7424790 6 SRR7424791 1 SRR7424792 6 SRR7424793 2 SRR7424794 5 SRR7424795 1 SRR7424796 6 SRR7424797 3 SRR7424798 4 SRR7424799 1 SRR7424800 4 SRR7424801 3 SRR7424802 1 SRR7424806 5 SRR7424808 3 SRR7424809 6 SRR7424810 6 SRR7424811 5 SRR7424812 2 SRR7424813 5 SRR7424814 6 SRR7424815 2 SRR7424816 6 SRR7424817 1 SRR7424818 1 SRR7424819 2 SRR7424820 3 SRR7424821 2 SRR7424823 2 SRR7424824 5

$clones_prevalence Experiment_1 Experiment_2 Experiment_3 Experiment_4 Total Clone_1 0.19863014 0.2612613 0.28888889 0.2500000 0.24421053 Clone_2 0.17808219 0.2702703 0.18888889 0.2421875 0.21894737 Clone_3 0.07534247 0.1081081 0.05555556 0.1171875 0.09052632 Clone_4 0.28082192 0.1981982 0.24444444 0.0625000 0.19578947 Clone_5 0.10273973 0.0000000 0.00000000 0.1640625 0.07578947 Clone_6 0.16438356 0.1621622 0.22222222 0.1640625 0.17473684

$relative_likelihoods Experiment_1 Experiment_2 Experiment_3 Experiment_4 -309.4589 -235.3992 -146.9536 -286.8702

$joint_likelihood [1] -241.1357

$clones_summary $clones_summary$Clone_1 [1] "ARPC2_2_218249894_C_T"

$clones_summary$Clone_2 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A"

$clones_summary$Clone_3 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "HNRNPC_14_21211843_C_T"

$clones_summary$Clone_4 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "COL1A2_7_94422978_C_A"

$clones_summary$Clone_5 [1] "ARPC2_2_218249894_C_T" "RPL5_1_92837514_C_G"

$clones_summary$Clone_6 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "COL1A2_7_94422978_C_A" [4] "CCT8_21_29063389_G_A"

$equivalent_solutions list()

$error_rates $error_rates$alpha [1] 0.10 0.05 0.05 0.05

$error_rates$beta [1] 0.10 0.05 0.05 0.05

marcoxa commented 4 years ago

Hi Bhavesh,

pretty interesting... Sorry for not being so responsive these days. As you may have surmised, we are in Italy, where things are a bit crazy.

You should prepare a more detailed project and submit it to NRNB. The NRNB will then select which project will be accepted.

All the best

Marco

On Sat, Mar 21, 2020 at 12:40 PM Bhavesh Narra notifications@github.com wrote:

print(inference) $B Root ARPC2_2_218249894_C_T PRAME_22_22551005_T_A HNRNPC_14_21211843_C_T Root 1 0 0 0 Clone_1 1 1 0 0 Clone_2 1 1 1 0 Clone_3 1 1 1 1 Clone_4 1 1 1 0 Clone_5 1 1 0 0 Clone_6 1 1 1 0 COL1A2_7_94422978_C_A RPL5_1_92837514_C_G CCT8_21_29063389_G_A Root 0 0 0 Clone_1 0 0 0 Clone_2 0 0 0 Clone_3 0 0 0 Clone_4 1 0 0 Clone_5 0 1 0 Clone_6 1 0 1

$C $C$Experiment_1 Clone SRR7424153 3 SRR7424154 4 SRR7424155 2 SRR7424156 1 SRR7424159 6 SRR7424160 4 SRR7424161 6 SRR7424162 4 SRR7424163 6 SRR7424164 6 SRR7424165 4 SRR7424166 4 SRR7424167 2 SRR7424168 2 SRR7424170 4 SRR7424172 1 SRR7424173 3 SRR7424174 4 SRR7424175 5 SRR7424176 4 SRR7424177 2 SRR7424178 1 SRR7424179 1 SRR7424180 2 SRR7424181 4 SRR7424182 1 SRR7424183 4 SRR7424184 6 SRR7424185 4 SRR7424186 5 SRR7424187 4 SRR7424188 1 SRR7424190 1 SRR7424191 4 SRR7424192 4 SRR7424193 1 SRR7424194 4 SRR7424195 6 SRR7424196 2 SRR7424197 4 SRR7424198 4 SRR7424199 6 SRR7424200 4 SRR7424201 1 SRR7424203 2 SRR7424204 6 SRR7424205 4 SRR7424206 2 SRR7424207 5 SRR7424208 2 SRR7424210 1 SRR7424211 2 SRR7424212 2 SRR7424213 6 SRR7424214 6 SRR7424215 3 SRR7424216 1 SRR7424217 4 SRR7424218 6 SRR7424219 4 SRR7424220 1 SRR7424221 4 SRR7424222 6 SRR7424223 1 SRR7424224 2 SRR7424226 4 SRR7424227 5 SRR7424228 2 SRR7424229 6 SRR7424230 4 SRR7424232 6 SRR7424233 4 SRR7424234 2 SRR7424235 2 SRR7424237 6 SRR7424238 6 SRR7424239 2 SRR7424240 4 SRR7424241 4 SRR7424242 4 SRR7424243 1 SRR7424244 2 SRR7424245 4 SRR7424246 1 SRR7424247 2 SRR7424248 5 SRR7424249 2 SRR7424251 1 SRR7424252 3 SRR7424255 5 SRR7424257 1 SRR7424258 5 SRR7424259 5 SRR7424260 3 SRR7424261 4 SRR7424262 1 SRR7424265 6 SRR7424266 3 SRR7424267 4 SRR7424268 6 SRR7424269 1 SRR7424270 3 SRR7424271 1 SRR7424272 1 SRR7424273 4 SRR7424274 3 SRR7424275 2 SRR7424277 2 SRR7424278 6 SRR7424279 1 SRR7424280 3 SRR7424281 1 SRR7424282 4 SRR7424284 5 SRR7424285 1 SRR7424286 3 SRR7424287 4 SRR7424288 1 SRR7424289 6 SRR7424290 5 SRR7424292 1 SRR7424293 4 SRR7424294 2 SRR7424295 2 SRR7424296 4 SRR7424297 4 SRR7424298 5 SRR7424300 4 SRR7424302 1 SRR7424303 6 SRR7424304 5 SRR7424305 6 SRR7424306 2 SRR7424307 6 SRR7424308 5 SRR7424309 1 SRR7424310 4 SRR7424311 5 SRR7424312 3 SRR7424313 2 SRR7424314 2 SRR7424318 1 SRR7424319 4 SRR7424320 5 SRR7424321 4 SRR7424322 6

$C$Experiment_2 Clone SRR7424324 6 SRR7424325 6 SRR7424326 4 SRR7424327 4 SRR7424328 6 SRR7424329 6 SRR7424330 4 SRR7424331 3 SRR7424332 6 SRR7424333 6 SRR7424335 1 SRR7424336 6 SRR7424337 2 SRR7424339 2 SRR7424340 1 SRR7424341 1 SRR7424342 3 SRR7424344 1 SRR7424345 4 SRR7424346 4 SRR7424347 1 SRR7424348 2 SRR7424349 2 SRR7424350 2 SRR7424352 4 SRR7424353 2 SRR7424354 2 SRR7424355 1 SRR7424356 1 SRR7424357 4 SRR7424358 1 SRR7424359 6 SRR7424360 4 SRR7424361 1 SRR7424363 6 SRR7424364 2 SRR7424365 4 SRR7424366 2 SRR7424367 4 SRR7424368 3 SRR7424369 3 SRR7424370 2 SRR7424371 1 SRR7424372 3 SRR7424375 4 SRR7424376 6 SRR7424379 2 SRR7424381 6 SRR7424382 2 SRR7424385 3 SRR7424386 3 SRR7424387 2 SRR7424388 6 SRR7424389 6 SRR7424390 1 SRR7424391 2 SRR7424395 1 SRR7424396 2 SRR7424397 4 SRR7424398 2 SRR7424399 1 SRR7424400 2 SRR7424401 4 SRR7424402 4 SRR7424403 1 SRR7424404 2 SRR7424405 1 SRR7424406 4 SRR7424407 4 SRR7424408 1 SRR7424409 6 SRR7424411 6 SRR7424412 4 SRR7424413 4 SRR7424416 2 SRR7424417 1 SRR7424419 2 SRR7424420 3 SRR7424423 4 SRR7424424 4 SRR7424425 3 SRR7424426 4 SRR7424430 1 SRR7424431 2 SRR7424434 2 SRR7424435 2 SRR7424437 3 SRR7424438 2 SRR7424441 1 SRR7424442 1 SRR7424444 1 SRR7424445 6 SRR7424450 1 SRR7424451 1 SRR7424452 2 SRR7424453 4 SRR7424454 2 SRR7424455 1 SRR7424457 1 SRR7424460 1 SRR7424463 2 SRR7424464 2 SRR7424465 6 SRR7424466 2 SRR7424468 3 SRR7424470 1 SRR7424471 6 SRR7424472 2 SRR7424473 3 SRR7424475 1 SRR7424476 1

$C$Experiment_3 Clone SRR7424479 3 SRR7424480 4 SRR7424482 4 SRR7424484 4 SRR7424485 4 SRR7424486 1 SRR7424487 1 SRR7424488 4 SRR7424489 6 SRR7424491 6 SRR7424493 4 SRR7424494 1 SRR7424497 1 SRR7424498 4 SRR7424499 4 SRR7424505 2 SRR7424506 3 SRR7424507 2 SRR7424509 1 SRR7424512 2 SRR7424515 1 SRR7424517 1 SRR7424518 2 SRR7424523 2 SRR7424524 2 SRR7424528 6 SRR7424529 2 SRR7424530 3 SRR7424532 4 SRR7424538 1 SRR7424543 1 SRR7424544 4 SRR7424545 2 SRR7424546 1 SRR7424554 6 SRR7424561 2 SRR7424565 2 SRR7424566 1 SRR7424567 1 SRR7424569 6 SRR7424571 2 SRR7424577 4 SRR7424579 6 SRR7424580 6 SRR7424583 2 SRR7424584 6 SRR7424585 2 SRR7424586 1 SRR7424587 6 SRR7424591 4 SRR7424592 1 SRR7424593 2 SRR7424595 4 SRR7424596 4 SRR7424597 4 SRR7424598 1 SRR7424600 6 SRR7424603 1 SRR7424605 1 SRR7424607 1 SRR7424608 6 SRR7424611 4 SRR7424614 6 SRR7424616 1 SRR7424618 2 SRR7424619 4 SRR7424620 3 SRR7424624 1 SRR7424628 6 SRR7424630 1 SRR7424631 4 SRR7424632 1 SRR7424634 6 SRR7424636 2 SRR7424638 1 SRR7424642 4 SRR7424645 3 SRR7424646 6 SRR7424647 4 SRR7424648 1 SRR7424649 6 SRR7424653 6 SRR7424656 1 SRR7424660 6 SRR7424662 4 SRR7424664 6 SRR7424665 6 SRR7424666 1 SRR7424671 2 SRR7424673 4

$C$Experiment_4 Clone SRR7424678 1 SRR7424680 6 SRR7424681 2 SRR7424682 4 SRR7424684 1 SRR7424685 1 SRR7424686 2 SRR7424687 1 SRR7424688 4 SRR7424689 1 SRR7424691 4 SRR7424692 4 SRR7424693 3 SRR7424694 1 SRR7424695 1 SRR7424696 6 SRR7424697 6 SRR7424698 3 SRR7424699 6 SRR7424700 3 SRR7424701 5 SRR7424702 2 SRR7424703 1 SRR7424705 6 SRR7424706 2 SRR7424707 6 SRR7424708 6 SRR7424709 2 SRR7424710 1 SRR7424711 2 SRR7424712 2 SRR7424713 3 SRR7424714 1 SRR7424715 2 SRR7424716 1 SRR7424717 1 SRR7424719 3 SRR7424721 1 SRR7424722 1 SRR7424723 2 SRR7424724 4 SRR7424725 5 SRR7424726 2 SRR7424727 1 SRR7424728 2 SRR7424729 1 SRR7424730 4 SRR7424731 2 SRR7424732 5 SRR7424733 6 SRR7424734 3 SRR7424735 1 SRR7424736 1 SRR7424737 2 SRR7424738 2 SRR7424739 2 SRR7424740 1 SRR7424741 2 SRR7424742 5 SRR7424743 2 SRR7424744 3 SRR7424745 6 SRR7424746 1 SRR7424747 6 SRR7424748 2 SRR7424749 1 SRR7424750 5 SRR7424751 6 SRR7424753 5 SRR7424754 5 SRR7424755 5 SRR7424756 2 SRR7424757 5 SRR7424758 1 SRR7424759 5 SRR7424760 2 SRR7424761 5 SRR7424762 1 SRR7424763 2 SRR7424764 5 SRR7424765 5 SRR7424766 3 SRR7424768 3 SRR7424769 1 SRR7424770 6 SRR7424772 5 SRR7424774 6 SRR7424775 6 SRR7424778 2 SRR7424779 5 SRR7424780 5 SRR7424781 3 SRR7424784 2 SRR7424785 2 SRR7424786 1 SRR7424787 3 SRR7424788 1 SRR7424789 2 SRR7424790 6 SRR7424791 1 SRR7424792 6 SRR7424793 2 SRR7424794 5 SRR7424795 1 SRR7424796 6 SRR7424797 3 SRR7424798 4 SRR7424799 1 SRR7424800 4 SRR7424801 3 SRR7424802 1 SRR7424806 5 SRR7424808 3 SRR7424809 6 SRR7424810 6 SRR7424811 5 SRR7424812 2 SRR7424813 5 SRR7424814 6 SRR7424815 2 SRR7424816 6 SRR7424817 1 SRR7424818 1 SRR7424819 2 SRR7424820 3 SRR7424821 2 SRR7424823 2 SRR7424824 5

$clones_prevalence Experiment_1 Experiment_2 Experiment_3 Experiment_4 Total Clone_1 0.19863014 0.2612613 0.28888889 0.2500000 0.24421053 Clone_2 0.17808219 0.2702703 0.18888889 0.2421875 0.21894737 Clone_3 0.07534247 0.1081081 0.05555556 0.1171875 0.09052632 Clone_4 0.28082192 0.1981982 0.24444444 0.0625000 0.19578947 Clone_5 0.10273973 0.0000000 0.00000000 0.1640625 0.07578947 Clone_6 0.16438356 0.1621622 0.22222222 0.1640625 0.17473684

$relative_likelihoods Experiment_1 Experiment_2 Experiment_3 Experiment_4 -309.4589 -235.3992 -146.9536 -286.8702

$joint_likelihood [1] -241.1357

$clones_summary $clones_summary$Clone_1 [1] "ARPC2_2_218249894_C_T"

$clones_summary$Clone_2 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A"

$clones_summary$Clone_3 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "HNRNPC_14_21211843_C_T"

$clones_summary$Clone_4 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "COL1A2_7_94422978_C_A"

$clones_summary$Clone_5 [1] "ARPC2_2_218249894_C_T" "RPL5_1_92837514_C_G"

$clones_summary$Clone_6 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "COL1A2_7_94422978_C_A" [4] "CCT8_21_29063389_G_A"

$equivalent_solutions list()

$error_rates $error_rates$alpha [1] 0.10 0.05 0.05 0.05

$error_rates$beta [1] 0.10 0.05 0.05 0.05

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/147#issuecomment-602032227, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAD5SWTFLYQJZZMY4CUAM5TRISRUXANCNFSM4KLWVPGA .

-- Marco Antoniotti Somewhere over the Rainbow

bhaveshnarra commented 4 years ago

Hi @marcoxa , I hope you guys are safe. Thanks for taking out time to reply in these crazy circumstances. Stay Safe.

sauravhiremath commented 4 years ago

Hey Marco,

I really hope you and your families are safe there.

It's a hard time, but it will pass. Stay safe

On Tue, 24 Mar, 2020, 8:08 pm Marco Antoniotti, notifications@github.com wrote:

Hi Bhavesh,

pretty interesting... Sorry for not being so responsive these days. As you may have surmised, we are in Italy, where things are a bit crazy.

You should prepare a more detailed project and submit it to NRNB. The NRNB will then select which project will be accepted.

All the best

Marco

On Sat, Mar 21, 2020 at 12:40 PM Bhavesh Narra notifications@github.com wrote:

print(inference) $B Root ARPC2_2_218249894_C_T PRAME_22_22551005_T_A HNRNPC_14_21211843_C_T Root 1 0 0 0 Clone_1 1 1 0 0 Clone_2 1 1 1 0 Clone_3 1 1 1 1 Clone_4 1 1 1 0 Clone_5 1 1 0 0 Clone_6 1 1 1 0 COL1A2_7_94422978_C_A RPL5_1_92837514_C_G CCT8_21_29063389_G_A Root 0 0 0 Clone_1 0 0 0 Clone_2 0 0 0 Clone_3 0 0 0 Clone_4 1 0 0 Clone_5 0 1 0 Clone_6 1 0 1

$C $C$Experiment_1 Clone SRR7424153 3 SRR7424154 4 SRR7424155 2 SRR7424156 1 SRR7424159 6 SRR7424160 4 SRR7424161 6 SRR7424162 4 SRR7424163 6 SRR7424164 6 SRR7424165 4 SRR7424166 4 SRR7424167 2 SRR7424168 2 SRR7424170 4 SRR7424172 1 SRR7424173 3 SRR7424174 4 SRR7424175 5 SRR7424176 4 SRR7424177 2 SRR7424178 1 SRR7424179 1 SRR7424180 2 SRR7424181 4 SRR7424182 1 SRR7424183 4 SRR7424184 6 SRR7424185 4 SRR7424186 5 SRR7424187 4 SRR7424188 1 SRR7424190 1 SRR7424191 4 SRR7424192 4 SRR7424193 1 SRR7424194 4 SRR7424195 6 SRR7424196 2 SRR7424197 4 SRR7424198 4 SRR7424199 6 SRR7424200 4 SRR7424201 1 SRR7424203 2 SRR7424204 6 SRR7424205 4 SRR7424206 2 SRR7424207 5 SRR7424208 2 SRR7424210 1 SRR7424211 2 SRR7424212 2 SRR7424213 6 SRR7424214 6 SRR7424215 3 SRR7424216 1 SRR7424217 4 SRR7424218 6 SRR7424219 4 SRR7424220 1 SRR7424221 4 SRR7424222 6 SRR7424223 1 SRR7424224 2 SRR7424226 4 SRR7424227 5 SRR7424228 2 SRR7424229 6 SRR7424230 4 SRR7424232 6 SRR7424233 4 SRR7424234 2 SRR7424235 2 SRR7424237 6 SRR7424238 6 SRR7424239 2 SRR7424240 4 SRR7424241 4 SRR7424242 4 SRR7424243 1 SRR7424244 2 SRR7424245 4 SRR7424246 1 SRR7424247 2 SRR7424248 5 SRR7424249 2 SRR7424251 1 SRR7424252 3 SRR7424255 5 SRR7424257 1 SRR7424258 5 SRR7424259 5 SRR7424260 3 SRR7424261 4 SRR7424262 1 SRR7424265 6 SRR7424266 3 SRR7424267 4 SRR7424268 6 SRR7424269 1 SRR7424270 3 SRR7424271 1 SRR7424272 1 SRR7424273 4 SRR7424274 3 SRR7424275 2 SRR7424277 2 SRR7424278 6 SRR7424279 1 SRR7424280 3 SRR7424281 1 SRR7424282 4 SRR7424284 5 SRR7424285 1 SRR7424286 3 SRR7424287 4 SRR7424288 1 SRR7424289 6 SRR7424290 5 SRR7424292 1 SRR7424293 4 SRR7424294 2 SRR7424295 2 SRR7424296 4 SRR7424297 4 SRR7424298 5 SRR7424300 4 SRR7424302 1 SRR7424303 6 SRR7424304 5 SRR7424305 6 SRR7424306 2 SRR7424307 6 SRR7424308 5 SRR7424309 1 SRR7424310 4 SRR7424311 5 SRR7424312 3 SRR7424313 2 SRR7424314 2 SRR7424318 1 SRR7424319 4 SRR7424320 5 SRR7424321 4 SRR7424322 6

$C$Experiment_2 Clone SRR7424324 6 SRR7424325 6 SRR7424326 4 SRR7424327 4 SRR7424328 6 SRR7424329 6 SRR7424330 4 SRR7424331 3 SRR7424332 6 SRR7424333 6 SRR7424335 1 SRR7424336 6 SRR7424337 2 SRR7424339 2 SRR7424340 1 SRR7424341 1 SRR7424342 3 SRR7424344 1 SRR7424345 4 SRR7424346 4 SRR7424347 1 SRR7424348 2 SRR7424349 2 SRR7424350 2 SRR7424352 4 SRR7424353 2 SRR7424354 2 SRR7424355 1 SRR7424356 1 SRR7424357 4 SRR7424358 1 SRR7424359 6 SRR7424360 4 SRR7424361 1 SRR7424363 6 SRR7424364 2 SRR7424365 4 SRR7424366 2 SRR7424367 4 SRR7424368 3 SRR7424369 3 SRR7424370 2 SRR7424371 1 SRR7424372 3 SRR7424375 4 SRR7424376 6 SRR7424379 2 SRR7424381 6 SRR7424382 2 SRR7424385 3 SRR7424386 3 SRR7424387 2 SRR7424388 6 SRR7424389 6 SRR7424390 1 SRR7424391 2 SRR7424395 1 SRR7424396 2 SRR7424397 4 SRR7424398 2 SRR7424399 1 SRR7424400 2 SRR7424401 4 SRR7424402 4 SRR7424403 1 SRR7424404 2 SRR7424405 1 SRR7424406 4 SRR7424407 4 SRR7424408 1 SRR7424409 6 SRR7424411 6 SRR7424412 4 SRR7424413 4 SRR7424416 2 SRR7424417 1 SRR7424419 2 SRR7424420 3 SRR7424423 4 SRR7424424 4 SRR7424425 3 SRR7424426 4 SRR7424430 1 SRR7424431 2 SRR7424434 2 SRR7424435 2 SRR7424437 3 SRR7424438 2 SRR7424441 1 SRR7424442 1 SRR7424444 1 SRR7424445 6 SRR7424450 1 SRR7424451 1 SRR7424452 2 SRR7424453 4 SRR7424454 2 SRR7424455 1 SRR7424457 1 SRR7424460 1 SRR7424463 2 SRR7424464 2 SRR7424465 6 SRR7424466 2 SRR7424468 3 SRR7424470 1 SRR7424471 6 SRR7424472 2 SRR7424473 3 SRR7424475 1 SRR7424476 1

$C$Experiment_3 Clone SRR7424479 3 SRR7424480 4 SRR7424482 4 SRR7424484 4 SRR7424485 4 SRR7424486 1 SRR7424487 1 SRR7424488 4 SRR7424489 6 SRR7424491 6 SRR7424493 4 SRR7424494 1 SRR7424497 1 SRR7424498 4 SRR7424499 4 SRR7424505 2 SRR7424506 3 SRR7424507 2 SRR7424509 1 SRR7424512 2 SRR7424515 1 SRR7424517 1 SRR7424518 2 SRR7424523 2 SRR7424524 2 SRR7424528 6 SRR7424529 2 SRR7424530 3 SRR7424532 4 SRR7424538 1 SRR7424543 1 SRR7424544 4 SRR7424545 2 SRR7424546 1 SRR7424554 6 SRR7424561 2 SRR7424565 2 SRR7424566 1 SRR7424567 1 SRR7424569 6 SRR7424571 2 SRR7424577 4 SRR7424579 6 SRR7424580 6 SRR7424583 2 SRR7424584 6 SRR7424585 2 SRR7424586 1 SRR7424587 6 SRR7424591 4 SRR7424592 1 SRR7424593 2 SRR7424595 4 SRR7424596 4 SRR7424597 4 SRR7424598 1 SRR7424600 6 SRR7424603 1 SRR7424605 1 SRR7424607 1 SRR7424608 6 SRR7424611 4 SRR7424614 6 SRR7424616 1 SRR7424618 2 SRR7424619 4 SRR7424620 3 SRR7424624 1 SRR7424628 6 SRR7424630 1 SRR7424631 4 SRR7424632 1 SRR7424634 6 SRR7424636 2 SRR7424638 1 SRR7424642 4 SRR7424645 3 SRR7424646 6 SRR7424647 4 SRR7424648 1 SRR7424649 6 SRR7424653 6 SRR7424656 1 SRR7424660 6 SRR7424662 4 SRR7424664 6 SRR7424665 6 SRR7424666 1 SRR7424671 2 SRR7424673 4

$C$Experiment_4 Clone SRR7424678 1 SRR7424680 6 SRR7424681 2 SRR7424682 4 SRR7424684 1 SRR7424685 1 SRR7424686 2 SRR7424687 1 SRR7424688 4 SRR7424689 1 SRR7424691 4 SRR7424692 4 SRR7424693 3 SRR7424694 1 SRR7424695 1 SRR7424696 6 SRR7424697 6 SRR7424698 3 SRR7424699 6 SRR7424700 3 SRR7424701 5 SRR7424702 2 SRR7424703 1 SRR7424705 6 SRR7424706 2 SRR7424707 6 SRR7424708 6 SRR7424709 2 SRR7424710 1 SRR7424711 2 SRR7424712 2 SRR7424713 3 SRR7424714 1 SRR7424715 2 SRR7424716 1 SRR7424717 1 SRR7424719 3 SRR7424721 1 SRR7424722 1 SRR7424723 2 SRR7424724 4 SRR7424725 5 SRR7424726 2 SRR7424727 1 SRR7424728 2 SRR7424729 1 SRR7424730 4 SRR7424731 2 SRR7424732 5 SRR7424733 6 SRR7424734 3 SRR7424735 1 SRR7424736 1 SRR7424737 2 SRR7424738 2 SRR7424739 2 SRR7424740 1 SRR7424741 2 SRR7424742 5 SRR7424743 2 SRR7424744 3 SRR7424745 6 SRR7424746 1 SRR7424747 6 SRR7424748 2 SRR7424749 1 SRR7424750 5 SRR7424751 6 SRR7424753 5 SRR7424754 5 SRR7424755 5 SRR7424756 2 SRR7424757 5 SRR7424758 1 SRR7424759 5 SRR7424760 2 SRR7424761 5 SRR7424762 1 SRR7424763 2 SRR7424764 5 SRR7424765 5 SRR7424766 3 SRR7424768 3 SRR7424769 1 SRR7424770 6 SRR7424772 5 SRR7424774 6 SRR7424775 6 SRR7424778 2 SRR7424779 5 SRR7424780 5 SRR7424781 3 SRR7424784 2 SRR7424785 2 SRR7424786 1 SRR7424787 3 SRR7424788 1 SRR7424789 2 SRR7424790 6 SRR7424791 1 SRR7424792 6 SRR7424793 2 SRR7424794 5 SRR7424795 1 SRR7424796 6 SRR7424797 3 SRR7424798 4 SRR7424799 1 SRR7424800 4 SRR7424801 3 SRR7424802 1 SRR7424806 5 SRR7424808 3 SRR7424809 6 SRR7424810 6 SRR7424811 5 SRR7424812 2 SRR7424813 5 SRR7424814 6 SRR7424815 2 SRR7424816 6 SRR7424817 1 SRR7424818 1 SRR7424819 2 SRR7424820 3 SRR7424821 2 SRR7424823 2 SRR7424824 5

$clones_prevalence Experiment_1 Experiment_2 Experiment_3 Experiment_4 Total Clone_1 0.19863014 0.2612613 0.28888889 0.2500000 0.24421053 Clone_2 0.17808219 0.2702703 0.18888889 0.2421875 0.21894737 Clone_3 0.07534247 0.1081081 0.05555556 0.1171875 0.09052632 Clone_4 0.28082192 0.1981982 0.24444444 0.0625000 0.19578947 Clone_5 0.10273973 0.0000000 0.00000000 0.1640625 0.07578947 Clone_6 0.16438356 0.1621622 0.22222222 0.1640625 0.17473684

$relative_likelihoods Experiment_1 Experiment_2 Experiment_3 Experiment_4 -309.4589 -235.3992 -146.9536 -286.8702

$joint_likelihood [1] -241.1357

$clones_summary $clones_summary$Clone_1 [1] "ARPC2_2_218249894_C_T"

$clones_summary$Clone_2 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A"

$clones_summary$Clone_3 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "HNRNPC_14_21211843_C_T"

$clones_summary$Clone_4 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "COL1A2_7_94422978_C_A"

$clones_summary$Clone_5 [1] "ARPC2_2_218249894_C_T" "RPL5_1_92837514_C_G"

$clones_summary$Clone_6 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "COL1A2_7_94422978_C_A" [4] "CCT8_21_29063389_G_A"

$equivalent_solutions list()

$error_rates $error_rates$alpha [1] 0.10 0.05 0.05 0.05

$error_rates$beta [1] 0.10 0.05 0.05 0.05

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/nrnb/GoogleSummerOfCode/issues/147#issuecomment-602032227 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAD5SWTFLYQJZZMY4CUAM5TRISRUXANCNFSM4KLWVPGA

.

-- Marco Antoniotti Somewhere over the Rainbow

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bhaveshnarra commented 4 years ago

Hi @marcoxa , @alexgraudenzi , @danro9685 I have shared my draft proposal if you guys can share your thoughts I would be grateful.

marcoxa commented 4 years ago

Thank you.

Be safe yourself.

Don't forget to submit your project to NRNB.

All the best

Marco

On Tue, Mar 24, 2020 at 6:11 PM Saurav M H notifications@github.com wrote:

Hey Marco,

I really hope you and your families are safe there.

It's a hard time, but it will pass. Stay safe

On Tue, 24 Mar, 2020, 8:08 pm Marco Antoniotti, notifications@github.com wrote:

Hi Bhavesh,

pretty interesting... Sorry for not being so responsive these days. As you may have surmised, we are in Italy, where things are a bit crazy.

You should prepare a more detailed project and submit it to NRNB. The NRNB will then select which project will be accepted.

All the best

Marco

On Sat, Mar 21, 2020 at 12:40 PM Bhavesh Narra <notifications@github.com

wrote:

print(inference) $B Root ARPC2_2_218249894_C_T PRAME_22_22551005_T_A HNRNPC_14_21211843_C_T Root 1 0 0 0 Clone_1 1 1 0 0 Clone_2 1 1 1 0 Clone_3 1 1 1 1 Clone_4 1 1 1 0 Clone_5 1 1 0 0 Clone_6 1 1 1 0 COL1A2_7_94422978_C_A RPL5_1_92837514_C_G CCT8_21_29063389_G_A Root 0 0 0 Clone_1 0 0 0 Clone_2 0 0 0 Clone_3 0 0 0 Clone_4 1 0 0 Clone_5 0 1 0 Clone_6 1 0 1

$C $C$Experiment_1 Clone SRR7424153 3 SRR7424154 4 SRR7424155 2 SRR7424156 1 SRR7424159 6 SRR7424160 4 SRR7424161 6 SRR7424162 4 SRR7424163 6 SRR7424164 6 SRR7424165 4 SRR7424166 4 SRR7424167 2 SRR7424168 2 SRR7424170 4 SRR7424172 1 SRR7424173 3 SRR7424174 4 SRR7424175 5 SRR7424176 4 SRR7424177 2 SRR7424178 1 SRR7424179 1 SRR7424180 2 SRR7424181 4 SRR7424182 1 SRR7424183 4 SRR7424184 6 SRR7424185 4 SRR7424186 5 SRR7424187 4 SRR7424188 1 SRR7424190 1 SRR7424191 4 SRR7424192 4 SRR7424193 1 SRR7424194 4 SRR7424195 6 SRR7424196 2 SRR7424197 4 SRR7424198 4 SRR7424199 6 SRR7424200 4 SRR7424201 1 SRR7424203 2 SRR7424204 6 SRR7424205 4 SRR7424206 2 SRR7424207 5 SRR7424208 2 SRR7424210 1 SRR7424211 2 SRR7424212 2 SRR7424213 6 SRR7424214 6 SRR7424215 3 SRR7424216 1 SRR7424217 4 SRR7424218 6 SRR7424219 4 SRR7424220 1 SRR7424221 4 SRR7424222 6 SRR7424223 1 SRR7424224 2 SRR7424226 4 SRR7424227 5 SRR7424228 2 SRR7424229 6 SRR7424230 4 SRR7424232 6 SRR7424233 4 SRR7424234 2 SRR7424235 2 SRR7424237 6 SRR7424238 6 SRR7424239 2 SRR7424240 4 SRR7424241 4 SRR7424242 4 SRR7424243 1 SRR7424244 2 SRR7424245 4 SRR7424246 1 SRR7424247 2 SRR7424248 5 SRR7424249 2 SRR7424251 1 SRR7424252 3 SRR7424255 5 SRR7424257 1 SRR7424258 5 SRR7424259 5 SRR7424260 3 SRR7424261 4 SRR7424262 1 SRR7424265 6 SRR7424266 3 SRR7424267 4 SRR7424268 6 SRR7424269 1 SRR7424270 3 SRR7424271 1 SRR7424272 1 SRR7424273 4 SRR7424274 3 SRR7424275 2 SRR7424277 2 SRR7424278 6 SRR7424279 1 SRR7424280 3 SRR7424281 1 SRR7424282 4 SRR7424284 5 SRR7424285 1 SRR7424286 3 SRR7424287 4 SRR7424288 1 SRR7424289 6 SRR7424290 5 SRR7424292 1 SRR7424293 4 SRR7424294 2 SRR7424295 2 SRR7424296 4 SRR7424297 4 SRR7424298 5 SRR7424300 4 SRR7424302 1 SRR7424303 6 SRR7424304 5 SRR7424305 6 SRR7424306 2 SRR7424307 6 SRR7424308 5 SRR7424309 1 SRR7424310 4 SRR7424311 5 SRR7424312 3 SRR7424313 2 SRR7424314 2 SRR7424318 1 SRR7424319 4 SRR7424320 5 SRR7424321 4 SRR7424322 6

$C$Experiment_2 Clone SRR7424324 6 SRR7424325 6 SRR7424326 4 SRR7424327 4 SRR7424328 6 SRR7424329 6 SRR7424330 4 SRR7424331 3 SRR7424332 6 SRR7424333 6 SRR7424335 1 SRR7424336 6 SRR7424337 2 SRR7424339 2 SRR7424340 1 SRR7424341 1 SRR7424342 3 SRR7424344 1 SRR7424345 4 SRR7424346 4 SRR7424347 1 SRR7424348 2 SRR7424349 2 SRR7424350 2 SRR7424352 4 SRR7424353 2 SRR7424354 2 SRR7424355 1 SRR7424356 1 SRR7424357 4 SRR7424358 1 SRR7424359 6 SRR7424360 4 SRR7424361 1 SRR7424363 6 SRR7424364 2 SRR7424365 4 SRR7424366 2 SRR7424367 4 SRR7424368 3 SRR7424369 3 SRR7424370 2 SRR7424371 1 SRR7424372 3 SRR7424375 4 SRR7424376 6 SRR7424379 2 SRR7424381 6 SRR7424382 2 SRR7424385 3 SRR7424386 3 SRR7424387 2 SRR7424388 6 SRR7424389 6 SRR7424390 1 SRR7424391 2 SRR7424395 1 SRR7424396 2 SRR7424397 4 SRR7424398 2 SRR7424399 1 SRR7424400 2 SRR7424401 4 SRR7424402 4 SRR7424403 1 SRR7424404 2 SRR7424405 1 SRR7424406 4 SRR7424407 4 SRR7424408 1 SRR7424409 6 SRR7424411 6 SRR7424412 4 SRR7424413 4 SRR7424416 2 SRR7424417 1 SRR7424419 2 SRR7424420 3 SRR7424423 4 SRR7424424 4 SRR7424425 3 SRR7424426 4 SRR7424430 1 SRR7424431 2 SRR7424434 2 SRR7424435 2 SRR7424437 3 SRR7424438 2 SRR7424441 1 SRR7424442 1 SRR7424444 1 SRR7424445 6 SRR7424450 1 SRR7424451 1 SRR7424452 2 SRR7424453 4 SRR7424454 2 SRR7424455 1 SRR7424457 1 SRR7424460 1 SRR7424463 2 SRR7424464 2 SRR7424465 6 SRR7424466 2 SRR7424468 3 SRR7424470 1 SRR7424471 6 SRR7424472 2 SRR7424473 3 SRR7424475 1 SRR7424476 1

$C$Experiment_3 Clone SRR7424479 3 SRR7424480 4 SRR7424482 4 SRR7424484 4 SRR7424485 4 SRR7424486 1 SRR7424487 1 SRR7424488 4 SRR7424489 6 SRR7424491 6 SRR7424493 4 SRR7424494 1 SRR7424497 1 SRR7424498 4 SRR7424499 4 SRR7424505 2 SRR7424506 3 SRR7424507 2 SRR7424509 1 SRR7424512 2 SRR7424515 1 SRR7424517 1 SRR7424518 2 SRR7424523 2 SRR7424524 2 SRR7424528 6 SRR7424529 2 SRR7424530 3 SRR7424532 4 SRR7424538 1 SRR7424543 1 SRR7424544 4 SRR7424545 2 SRR7424546 1 SRR7424554 6 SRR7424561 2 SRR7424565 2 SRR7424566 1 SRR7424567 1 SRR7424569 6 SRR7424571 2 SRR7424577 4 SRR7424579 6 SRR7424580 6 SRR7424583 2 SRR7424584 6 SRR7424585 2 SRR7424586 1 SRR7424587 6 SRR7424591 4 SRR7424592 1 SRR7424593 2 SRR7424595 4 SRR7424596 4 SRR7424597 4 SRR7424598 1 SRR7424600 6 SRR7424603 1 SRR7424605 1 SRR7424607 1 SRR7424608 6 SRR7424611 4 SRR7424614 6 SRR7424616 1 SRR7424618 2 SRR7424619 4 SRR7424620 3 SRR7424624 1 SRR7424628 6 SRR7424630 1 SRR7424631 4 SRR7424632 1 SRR7424634 6 SRR7424636 2 SRR7424638 1 SRR7424642 4 SRR7424645 3 SRR7424646 6 SRR7424647 4 SRR7424648 1 SRR7424649 6 SRR7424653 6 SRR7424656 1 SRR7424660 6 SRR7424662 4 SRR7424664 6 SRR7424665 6 SRR7424666 1 SRR7424671 2 SRR7424673 4

$C$Experiment_4 Clone SRR7424678 1 SRR7424680 6 SRR7424681 2 SRR7424682 4 SRR7424684 1 SRR7424685 1 SRR7424686 2 SRR7424687 1 SRR7424688 4 SRR7424689 1 SRR7424691 4 SRR7424692 4 SRR7424693 3 SRR7424694 1 SRR7424695 1 SRR7424696 6 SRR7424697 6 SRR7424698 3 SRR7424699 6 SRR7424700 3 SRR7424701 5 SRR7424702 2 SRR7424703 1 SRR7424705 6 SRR7424706 2 SRR7424707 6 SRR7424708 6 SRR7424709 2 SRR7424710 1 SRR7424711 2 SRR7424712 2 SRR7424713 3 SRR7424714 1 SRR7424715 2 SRR7424716 1 SRR7424717 1 SRR7424719 3 SRR7424721 1 SRR7424722 1 SRR7424723 2 SRR7424724 4 SRR7424725 5 SRR7424726 2 SRR7424727 1 SRR7424728 2 SRR7424729 1 SRR7424730 4 SRR7424731 2 SRR7424732 5 SRR7424733 6 SRR7424734 3 SRR7424735 1 SRR7424736 1 SRR7424737 2 SRR7424738 2 SRR7424739 2 SRR7424740 1 SRR7424741 2 SRR7424742 5 SRR7424743 2 SRR7424744 3 SRR7424745 6 SRR7424746 1 SRR7424747 6 SRR7424748 2 SRR7424749 1 SRR7424750 5 SRR7424751 6 SRR7424753 5 SRR7424754 5 SRR7424755 5 SRR7424756 2 SRR7424757 5 SRR7424758 1 SRR7424759 5 SRR7424760 2 SRR7424761 5 SRR7424762 1 SRR7424763 2 SRR7424764 5 SRR7424765 5 SRR7424766 3 SRR7424768 3 SRR7424769 1 SRR7424770 6 SRR7424772 5 SRR7424774 6 SRR7424775 6 SRR7424778 2 SRR7424779 5 SRR7424780 5 SRR7424781 3 SRR7424784 2 SRR7424785 2 SRR7424786 1 SRR7424787 3 SRR7424788 1 SRR7424789 2 SRR7424790 6 SRR7424791 1 SRR7424792 6 SRR7424793 2 SRR7424794 5 SRR7424795 1 SRR7424796 6 SRR7424797 3 SRR7424798 4 SRR7424799 1 SRR7424800 4 SRR7424801 3 SRR7424802 1 SRR7424806 5 SRR7424808 3 SRR7424809 6 SRR7424810 6 SRR7424811 5 SRR7424812 2 SRR7424813 5 SRR7424814 6 SRR7424815 2 SRR7424816 6 SRR7424817 1 SRR7424818 1 SRR7424819 2 SRR7424820 3 SRR7424821 2 SRR7424823 2 SRR7424824 5

$clones_prevalence Experiment_1 Experiment_2 Experiment_3 Experiment_4 Total Clone_1 0.19863014 0.2612613 0.28888889 0.2500000 0.24421053 Clone_2 0.17808219 0.2702703 0.18888889 0.2421875 0.21894737 Clone_3 0.07534247 0.1081081 0.05555556 0.1171875 0.09052632 Clone_4 0.28082192 0.1981982 0.24444444 0.0625000 0.19578947 Clone_5 0.10273973 0.0000000 0.00000000 0.1640625 0.07578947 Clone_6 0.16438356 0.1621622 0.22222222 0.1640625 0.17473684

$relative_likelihoods Experiment_1 Experiment_2 Experiment_3 Experiment_4 -309.4589 -235.3992 -146.9536 -286.8702

$joint_likelihood [1] -241.1357

$clones_summary $clones_summary$Clone_1 [1] "ARPC2_2_218249894_C_T"

$clones_summary$Clone_2 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A"

$clones_summary$Clone_3 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "HNRNPC_14_21211843_C_T"

$clones_summary$Clone_4 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "COL1A2_7_94422978_C_A"

$clones_summary$Clone_5 [1] "ARPC2_2_218249894_C_T" "RPL5_1_92837514_C_G"

$clones_summary$Clone_6 [1] "ARPC2_2_218249894_C_T" "PRAME_22_22551005_T_A" "COL1A2_7_94422978_C_A" [4] "CCT8_21_29063389_G_A"

$equivalent_solutions list()

$error_rates $error_rates$alpha [1] 0.10 0.05 0.05 0.05

$error_rates$beta [1] 0.10 0.05 0.05 0.05

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marcoxa commented 4 years ago

Hi Bhavesh

have you already submitted you project to NRNB? I do not seem to have seen it or got a link to it.

All the best

Marco

On Sun, Mar 29, 2020 at 4:28 PM Bhavesh Narra notifications@github.com wrote:

Hi @marcoxa https://github.com/marcoxa , @alexgraudenzi https://github.com/alexgraudenzi , @danro9685 https://github.com/danro9685 I have shared my draft proposal if you guys can share your thoughts I would be grateful.

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bhaveshnarra commented 4 years ago

Hi @marcoxa I have shared the draft link with NRNB I have still yet to submit it. I will mail the link to you just in case.

bhaveshnarra commented 4 years ago

Hi @marcoxa i shared the review link with you by mail kindly check it.

marcoxa commented 4 years ago

Hi Bhavesh

sorry, but I do not see the link. Could you post it here.

All the best

Marco

bhaveshnarra commented 4 years ago

Hi @marcoxa I am sorry but it would be pretty risky for me to post the proposal here. I shared it through the summer of code portal for NRNB. Could you just check through the google summer of code portal? I have enabled comment access for your email though. Just check your email as well (marco.antoniotti@unimib.it)you will have an invitation to comment for a google doc.

bhaveshnarra commented 4 years ago

I have just submitted the final proposal Kindly check if you can view it Now. I can still upload new one after making changes so feel free to comment here.

bhaveshnarra commented 4 years ago

Screenshot from 2020-03-31 08-09-31

marcoxa commented 4 years ago

Hi Bhavesh

I finally got access to your proposal. I will give you some feedback in the next few days. Sorry but it is crazy these days...

All the best

Marco

On Tue, Mar 31, 2020 at 4:40 AM Bhavesh Narra notifications@github.com wrote:

[image: Screenshot from 2020-03-31 08-09-31] https://user-images.githubusercontent.com/52484030/77981256-04393c00-7327-11ea-8296-3515eefcf047.png

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bhaveshnarra commented 4 years ago

Hi @marcoxa

Sure Marco I completely understand.

Bhavesh

marcoxa commented 4 years ago

Hi Bhavesh

great project. I hope you will make the cut. As you may know you are competing with other 48 students to get into ten-ish slots and there are also other people doing the evaluation.

If you get the slot, we'll have to discuss how to move onward. You should concentrate of cytoscape.js and its visual component.

All the best

Marco

On Sat, Apr 4, 2020 at 5:45 AM Bhavesh Narra notifications@github.com wrote:

Hi @marcoxa https://github.com/marcoxa

Sure Marco I completely understand.

Bhavesh

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bhaveshnarra commented 4 years ago

Hi @marcoxa ,

It means a great deal that you were able to review my proposal during these circumstances. The odds are a little intimidating but I hope we do well and I get a chance to work with you in the summer.

I will take your advice and focus on using cytoscape.js and all of its relevant features. While I wait for the announcement I will be working on cytoscape.js snippets.

khanspers commented 4 years ago

Active project for GSoC 2020, closing here.

marcoxa commented 4 years ago

Dear Bhavesh

welcome on board. First of all, can you send us a direct email? Also cc: my @unimib.it email in all communications. Moreover, on what Time Zone are you? with respect to CET?

We also have something more from NRNB which we need to look at and have you subscribe.

Let's write good software!

All the best

Marco

On Sat, Apr 18, 2020 at 6:21 AM Bhavesh Narra notifications@github.com wrote:

Hi @marcoxa https://github.com/marcoxa ,

It means a great deal that you were able to review my proposal during these circumstances. The odds are a little intimidating but I hope we do well and I get a chance to work with you in the summer.

I will take your advice and focus on using cytoscape.js and all of its relevant features. While I wait for the announcement I will be working on cytoscape.js snippets.

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bhaveshnarra commented 4 years ago

Hi Marco. So excited that we made it.

I will direct email you along with @alexgraudenzi , @danro9685 . My time zone is IST which is 3H 30 min ahead.

Here's to start of a great project.

Cheers

Bhavesh

bhaveshnarra commented 4 years ago

Hi Marco I just mailed you at your @unimib.it email from my university mail @pilani.bits-pilani.ac.in.

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