weberlab-hhu GeenuFF issues

weberlab-hhu / GeenuFF

Schema and API for a relational db that encodes gene models in an explicit, structured, and robust fashion.

GNU General Public License v3.0

6 stars 8 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Dependency on dustdas

#400 anthony-aylward opened 3 months ago
0
Remove dependency on dustdas

#399 anthony-aylward opened 3 months ago
0
Update requirements.txt

#398 haessar opened 6 months ago
0
Still need to implement backward match if fasta IDs are subset of gff IDs

#397 hjjansen opened 1 year ago
4
Add lenient parser mode

#396 alisandra opened 1 year ago
0
chromosomes can be longer than max string length in sqlite3 for a coordinate -> fix

#395 alisandra opened 2 years ago
0
Merge Multiple GFFs into one Sqlite3 file

#394 wyim-pgl closed 2 years ago
1
How to properly deal with RefSeq pseudogenes without transcript?

#393 soi opened 3 years ago
0
Properly handle non-coding genes

#392 alisandra opened 4 years ago
1
Export back to GFF3

#391 alisandra opened 4 years ago
0
Add Prokaryotic GFF Importer

#390 alisandra opened 4 years ago
0
Make sure import supports a few more common gff3 sources

#389 alisandra opened 4 years ago
0
save git commits even if run from outside of repository

#388 alisandra closed 4 years ago
1
Evaluate data augmentation that switches strands

#387 soi closed 4 years ago
1
Add test for data augmentation that switches strands

#386 soi closed 4 years ago
1
Add data augmentation that switches strands

#385 soi closed 4 years ago
1
Include all data by default in data sets

#384 soi closed 4 years ago
2
Evaluate double stranded data models

#383 soi closed 4 years ago
1
Write test for double stranded data generation

#382 soi closed 4 years ago
1
Somtimes predicted categories don't sum to one (overlap + ensembled)

#381 alisandra closed 4 years ago
2
Reorder/Merge Introduction

#380 soi closed 4 years ago
0
Write Abstract

#379 soi closed 4 years ago
0
Add species wise overlapping effect plots to supplement

#378 soi closed 4 years ago
0
Move supplement to extra doc

#377 soi closed 4 years ago
0
Change resolution and format of images

#376 soi closed 4 years ago
1
Write cover letter

#375 soi closed 4 years ago
0
Talk about our performance with respect to species family

#374 soi closed 4 years ago
0
Setup and document working Helixer example

#373 soi closed 4 years ago
0
Update Helixer docs

#372 soi closed 4 years ago
0
Resolve questionmarks in text

#371 soi closed 4 years ago
0
Add all hyperparameters to table

#370 soi closed 4 years ago
0
Boxplot image of us vs. Augustus

#369 soi closed 4 years ago
1
Model image

#368 soi closed 4 years ago
1
Evaluate animal models with longer input length only

#367 soi closed 4 years ago
0
Evaluate basic animal models

#366 soi closed 4 years ago
0
Evaluate basic plant models

#365 soi closed 4 years ago
0
Describe input of longer sequences in supplementary

#364 soi closed 4 years ago
0
Add full results (all classes) in supplementary material

#363 soi closed 4 years ago
0
Make phylogenetic plots

#362 soi closed 4 years ago
0
Make proper position wise bias plots

#361 soi closed 4 years ago
1
Describe the dilated cnn baseline in an appendix kind of way

#360 soi closed 4 years ago
0
Fill in overall results table

#359 soi closed 4 years ago
0
Write discussion of results

#358 soi closed 4 years ago
1
reduce memory usage during export to h5

#357 alisandra closed 4 years ago
0
Use efficient _genome_query and join for everything using _super_locus_query

#356 alisandra opened 4 years ago
0
Redo statistics after total error fix

#355 soi closed 4 years ago
0
Total bases are too high in statistics

#354 soi closed 4 years ago
1
Run all 20/50/100k long predictions locally and upload to the cluster

#353 soi closed 4 years ago
0
Fully evaluate best cnn baseline

#352 soi closed 4 years ago
0
Train good cnn baseline

#351 soi closed 4 years ago
0