Join the developer team

[lpantano]

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.

[FlorianThibord]

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

[jsimonas]

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

[arunhpatil]

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

[lpantano]

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!

[arunhpatil]

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

[jsimonas]

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>.

[FlorianThibord]

Hi all,
Thursday 22 works fine for me.

Thanks,
Florian

[lpantano]

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.

[lpantano]

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

[jsimonas]

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> .

[lpantano]

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!

[lpantano]

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

[lpantano]

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