Comments (6)
I am interested in it, but I think I can only test it.. I don't feel myself free enough in python..
from annotsv.
Hi Sergey,
Thanks for considering to test AnnotSV in Python. I keep that in mind.
Currently, new ideas/features to investigate in AnnotSV are piling up... and I can't achieve everything ;o(
So a Python implementation really makes sense for me, to encourage participation by everyone.
Help from someone experienced with Python is welcome.
Best,
Véronique
from annotsv.
AnnotSV is the best software I have ever used for SV annotation.
If AnnotSV implementation in Python, I will be interested in this nice and collaborative work.
from annotsv.
Hi LiPidong,
Thank you, it's nice to hear that you have found AnnotSV useful.
Can you contact me by email at [email protected]?
Best,
Véronique
from annotsv.
Hi!
This is an old thread, but I would like to add a question/suggestion here. I have recently been exploring various bioinformatics tools for CNV annotation, and it got me thinking about the possibility of having AnnotSV as an R package. I am reaching out to inquire if you have considered implementing AnnotSV as an R package.
I'm unsure whether it makes sense, considering the current AnnotSV tool works quite efficiently. Nevertheless, the R environment is widely used among researchers and provides a robust ecosystem for data analysis and visualization. AnnotSV as an R package could enhance its accessibility and usability within the R community and integrate AnnotSV in R-based analysis pipelines along other popular R packages, allowing seamless analysis workflows.
If you have not yet explored the idea of an R package for AnnotSV, I would be more than happy to offer my assistance. I have yet to gain experience developing R packages, but I'm proficient in R coding. I could contribute to the development efforts by adapting the existing codebase to R, creating appropriate documentation, or smoothly integrating existing R tools and data structures.
I appreciate the valuable work you have put into developing AnnotSV.
Best regards,
Alfredo Ortega, PhD.
University of Helsinki
from annotsv.
Hi Alfredo,
Thanks for your interest in AnnotSV ;o)
Actually, I never considered implementing AnnotSV as an R package and you are the first to submit the idea.
Unfortunately, I'm not proficient in R coding. And, as you can see with this old thread, I'm running out of time to implement AnnotSV in Python. So I won't be able to invest time in this R project.
However, I am open and interested in any new collaboration around AnnotSV. I love open science!
So feel free to adapt the existing codebase to R and create appropriate documentation. It will benefit the community.
However, keep in mind that this is a long-term investment, and that the R version should be updated in parallel with the Tcl version.
Best,
Véronique
from annotsv.
Related Issues (20)
- AnnotSV doesn't add the sample IDs causing variantconvert to fail HOT 13
- CNVs' ID modified in output file HOT 1
- AnnotSV Singularity on an HPC Error `command not found` HOT 24
- checkCOSMICfile update HOT 8
- Error with test Data during the install (requirements) HOT 5
- Installation of 3.6.6 is failing HOT 2
- Query on the allele frequency HOT 8
- Difference in results between "knotAnnotSV online" and "knotAnnotSV command-line" versions HOT 8
- VCF field format issue HOT 9
- Gnomad variant effect columns HOT 3
- [Improvement] Read HPO from phenopacket file HOT 1
- inversions lost HOT 2
- Conda (and container) version of AnnotSV runs into error when run with -hpo arg HOT 24
- gnomAD SV INS effect on ranking score / ACMG class HOT 2
- 'etc/AnnotSV/configfile' disable annotation function does not Work HOT 4
- SVinputFile too big HOT 5
- domain error: argument not in valid range HOT 11
- query on the results HOT 8
- gnomad V4 HOT 6
- PacBio pipeline structural variant annotations HOT 30
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