Join the developer team

Hi,

If you have experience with python or R, or you analyze small RNAseq data yourself, please consider to join us. We have several projects that are community-driven:

mirtop: python proxy to convert tools output to mirGFF3 and process those files for downstream analysis
mirGFF3_shiny: R shiny tool to analyze mirGFF3 files.

Comment here with your name and affiliation, and I will add you to the team.

We will have monthly meetings to coordinate efforts and the time investment is variable, from a couple of hours a month to weekly contributions.

Hi Lorena,
I am experienced with python and R and I will be happy to help. I am not familiar with shiny apps but this could be an opportunity to learn ;)

Name and affiliation:
Florian Thibord. INSERM, UMR_S 1219, Bordeaux Population Health Research Center, University of Bordeaux, Bordeaux, France

Hi Lorena,
I have experience in R and Shiny, I also work with miRNAs for quite awhile and would be happy to contribute.

Hi Lorena,

I have experience with small RNA analysis with basic scripting knowledge in Python and R. I will be happy to join the team.
Name: Arun Patil
Affiliation: Dept. of Pathology, Johns Hopkins University

Hi all,

thanks for joining us!

I have two dates in mind for the first meeting: Monday 19 at 10am (EST) or Thursday 22 at 10am (EST).

Can you let me know if that works for you all? If not I will send a doodle to get a common date and time.

Thanks!

Hi Lorena, Thursday 22 would be more convenient for me. Thank you, Arun.

…

On Mon, Aug 12, 2019 at 9:28 PM Lorena Pantano ***@***.***> wrote: Hi all, thanks for joining us! I have two dates in mind for the first meeting: Monday 19 at 10am (EST) or Thursday 22 at 10am (EST). Can you let me know if that works for you all? If not I will send a doodle to get a common date and time. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=ACMKKY6GEDQTQRGORAUOFGLQEGCCFA5CNFSM4IHF2QV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4C7Y5Y#issuecomment-520486007>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACMKKY6V4BS6D6YZM7CBGA3QEGCCFANCNFSM4IHF2QVQ> .

-- Arun H Patil, Ph.D. Institute of Bioinformatics Discoverer Building, 7th Floor International Tech Park Whitefield, Bangalore - 560 066 Karnataka, India. Mobile:(+91) 9964121551 Phone:(+91) 80-28416140 Fax: (+91) 80-28416132

Dear Lorena, For me Thursday would fit better as well. Greetings, Simonas

…

On 13. Aug 2019, at 06:55, Arun Patil ***@***.***> wrote: Hi Lorena, Thursday 22 would be more convenient for me. Thank you, Arun. On Mon, Aug 12, 2019 at 9:28 PM Lorena Pantano ***@***.***> wrote: > Hi all, > > thanks for joining us! > > I have two dates in mind for the first meeting: Monday 19 at 10am (EST) or > Thursday 22 at 10am (EST). > > Can you let me know if that works for you all? If not I will send a doodle > to get a common date and time. > > Thanks! > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#5?email_source=notifications&email_token=ACMKKY6GEDQTQRGORAUOFGLQEGCCFA5CNFSM4IHF2QV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4C7Y5Y#issuecomment-520486007>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ACMKKY6V4BS6D6YZM7CBGA3QEGCCFANCNFSM4IHF2QVQ> > . > -- Arun H Patil, Ph.D. Institute of Bioinformatics Discoverer Building, 7th Floor International Tech Park Whitefield, Bangalore - 560 066 Karnataka, India. Mobile:(+91) 9964121551 Phone:(+91) 80-28416140 Fax: (+91) 80-28416132 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=ABXA6ESFCBDI55KQB4X6KCDQEI5CZA5CNFSM4IHF2QV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4ERFYA#issuecomment-520688352>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABXA6EUXVJKW777ZSGEOAU3QEI5CZANCNFSM4IHF2QVQ>.

Hi all,
Thursday 22 works fine for me.

Thanks,
Florian

Thank you!. Then we will have a call on Thursday 22 at 10am EST, I will post the link when we are closer to the date.

Here there is the link to connect: https://zoom.us/j/553765969, see you in 50 minutes.

Dear all, I'm very sorry but I won't be able to make it today.

…

On Thu, Aug 22, 2019, 15:10 Lorena Pantano ***@***.***> wrote: Here there is the link to connect: https://zoom.us/j/553765969, see you in 50 minutes. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=ABXA6EW443B5DPVOENH2EX3QF2F25A5CNFSM4IHF2QV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD45BATQ#issuecomment-523898958>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABXA6EXVHSUUF5LHFIT6OZTQF2F25ANCNFSM4IHF2QVQ> .

Thank you for participate,

Florian: this is the pull request: MultiQC/MultiQC#788, from there you can go to the documentation and find how to test data, but please, let me know if something is not working.

Arun: this is the issue for the sqlite project:miRTop/mirtop#56

We can chat over: https://gitter.im/mirtop/devel

Meetings will be once a month, next one is on Setp-19: https://zoom.us/j/553765969

Thanks!

Thanks for coming!

Minutes:

PR is ongoing for SQL functions
mirtop module in multiqc is working as it is
SQL possible queries:
- query:
  - variants for this miRNA
  - variants with iso_5p, iso_3p
  - variants with more than N changes
  - variants with a FILTER value
  - variants with seed afected: iso_5p and iso_snv_seed and iso_add5p
- stats:
  - how many type of isomirs per mirna

Actions

send the biggest file I have for sql creation test: Lorena
make PR to DEV: Arun
Multiqc: Florian
- we should separate in three barplots (counts, mean, sum): xaxis are samples, colored by isomir type

Meetings will be once a month, next one is on Oct-17 10AM EST: https://zoom.us/j/553765969

Let's have a quick meeting today in 40 minutes:
https://zoom.us/j/553765969

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FlorianThibord commented on Jul 29, 2019

jsimonas commented on Jul 30, 2019

arunhpatil commented on Aug 1, 2019

lpantano commented on Aug 12, 2019

arunhpatil commented on Aug 13, 2019

jsimonas commented on Aug 13, 2019

FlorianThibord commented on Aug 13, 2019

lpantano commented on Aug 13, 2019

lpantano commented on Aug 22, 2019

jsimonas commented on Aug 22, 2019

lpantano commented on Aug 22, 2019

lpantano commented on Sep 19, 2019

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lpantano commented on Oct 17, 2019

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