lpantano commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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

arunhpatil commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

Hi Lorena,

Thursday 22 would be more convenient for me.

Thank you, Arun.

On Mon, Aug 12, 2019 at 9:28 PM Lorena Pantano notifications@github.com 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 https://github.com/miRTop/miRTOP.github.io/issues/5?email_source=notifications&email_token=ACMKKY6GEDQTQRGORAUOFGLQEGCCFA5CNFSM4IHF2QV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4C7Y5Y#issuecomment-520486007, or mute the thread https://github.com/notifications/unsubscribe-auth/ACMKKY6V4BS6D6YZM7CBGA3QEGCCFANCNFSM4IHF2QVQ .

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jsimonas commented 5 years ago

Dear Lorena,

For me Thursday would fit better as well.

Greetings, Simonas

On 13. Aug 2019, at 06:55, Arun Patil notifications@github.com 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 notifications@github.com 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 https://github.com/miRTop/miRTOP.github.io/issues/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 https://github.com/miRTop/miRTOP.github.io/issues/5?email_source=notifications&email_token=ABXA6ESFCBDI55KQB4X6KCDQEI5CZA5CNFSM4IHF2QV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4ERFYA#issuecomment-520688352, or mute the thread https://github.com/notifications/unsubscribe-auth/ABXA6EUXVJKW777ZSGEOAU3QEI5CZANCNFSM4IHF2QVQ.

FlorianThibord commented 5 years ago

Hi all, Thursday 22 works fine for me.

Thanks, Florian

lpantano commented 5 years ago

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 commented 5 years ago

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

jsimonas commented 5 years ago

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 notifications@github.com 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 https://github.com/miRTop/miRTOP.github.io/issues/5?email_source=notifications&email_token=ABXA6EW443B5DPVOENH2EX3QF2F25A5CNFSM4IHF2QV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD45BATQ#issuecomment-523898958, or mute the thread https://github.com/notifications/unsubscribe-auth/ABXA6EXVHSUUF5LHFIT6OZTQF2F25ANCNFSM4IHF2QVQ .

lpantano commented 5 years ago

Thank you for participate,

Florian: this is the pull request: https://github.com/ewels/MultiQC/pull/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:https://github.com/miRTop/mirtop/issues/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 commented 4 years ago

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 commented 4 years ago

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

miRTop / miRTOP.github.io

Join the developer team #5

Minutes:

Actions