Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / gagneurlab/MMSplice_MTSplice issues and pull requests

#71 - BUG: Colab notebook is broken

Issue - State: open - Opened by KuechlerO 5 months ago

#70 - BUG: VCF requirements not clearly stated & wrong seqnames derived

Issue - State: open - Opened by KuechlerO 5 months ago - 1 comment

#69 - kipoiseq problem

Issue - State: open - Opened by Eyulaochen 7 months ago

#68 - TSplice architecture

Issue - State: open - Opened by dbogdano 9 months ago

#67 - Version 2.4

Pull Request - State: closed - Opened by MuhammedHasan over 1 year ago

#66 - pypi_kipoiseq08

Pull Request - State: closed - Opened by MuhammedHasan over 1 year ago

#65 - intermediate kipoiseq version

Pull Request - State: open - Opened by WagnerNils over 1 year ago

#64 - 'chr' annotation in fasta and vcf can differ

Pull Request - State: open - Opened by WagnerNils over 1 year ago

#63 - How to interpret tissue specific results

Issue - State: open - Opened by AndreaG5 over 1 year ago - 1 comment

#62 - Bump wheel from 0.30.0 to 0.38.1

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#60 - running predictions with tensorflow is slow

Issue - State: open - Opened by dagap over 2 years ago

#59 - dependency_updates_sklearn_dropped v2.3

Pull Request - State: closed - Opened by MuhammedHasan almost 3 years ago - 1 comment

#58 - fix predict_save to parquet

Pull Request - State: closed - Opened by WagnerNils almost 3 years ago

#57 - Bump pip from 9.0.1 to 21.1

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#56 - model predictions in google collab

Issue - State: closed - Opened by pablo-baeza almost 3 years ago - 1 comment

#55 - added batch writer to parquet

Pull Request - State: closed - Opened by WagnerNils almost 3 years ago

#54 - Package dependencies don't overlap & trouble with google collab script

Issue - State: closed - Opened by bomansonja almost 3 years ago - 3 comments
Labels: bug

#53 - "stop iteration" trouble

Issue - State: open - Opened by rominageysels about 3 years ago - 2 comments

#52 - Conda package for MMsplice

Issue - State: open - Opened by bioinfo-K1 about 3 years ago - 1 comment
Labels: enhancement

#51 - Identifying the predicted types of splicing events

Issue - State: open - Opened by bioinfo-K1 about 3 years ago - 2 comments

#50 - Region support

Pull Request - State: closed - Opened by MuhammedHasan over 3 years ago
Labels: bug, enhancement, dependencies

#49 - Bump pip from 9.0.1 to 19.2

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#48 - Interpretation of Results

Issue - State: closed - Opened by astarr97 over 3 years ago - 2 comments

#47 - Used in non-model species?

Issue - State: closed - Opened by FarmOmics over 3 years ago - 1 comment

#46 - Error with running MMSplice - keras decode('utf-8')

Issue - State: closed - Opened by pj-sullivan over 3 years ago - 4 comments

#45 - Replace sklearn models with numpy implementation

Issue - State: closed - Opened by s6juncheng almost 4 years ago
Labels: enhancement

#44 - memory efficient use of pyranges

Pull Request - State: closed - Opened by s6juncheng about 4 years ago

#43 - MemoryError

Issue - State: closed - Opened by segoerge about 4 years ago - 17 comments

#42 - Controlling the number of threads

Issue - State: closed - Opened by tstohn about 4 years ago - 2 comments

#41 - Problem combining MMSplice module with custom annotation in VEP

Issue - State: closed - Opened by helenapersson about 4 years ago - 4 comments

#40 - error running example data - Input sequence acceptor intron length cannot be longer than the input sequence

Issue - State: closed - Opened by rhalperin about 4 years ago - 3 comments
Labels: question

#39 - Juntion dataloader bug

Pull Request - State: closed - Opened by MuhammedHasan over 4 years ago

#38 - Mtsplice

Pull Request - State: closed - Opened by MuhammedHasan over 4 years ago

#37 - Adding vcf/gtf chromosome name check

Issue - State: closed - Opened by nickhsmith over 4 years ago - 3 comments
Labels: enhancement

#36 - Error installing MMSplice

Issue - State: closed - Opened by dglemos over 4 years ago - 3 comments
Labels: question

#35 - fix in metadata for kipoi

Pull Request - State: closed - Opened by MuhammedHasan over 4 years ago

#34 - bug fix caused by kipoiseq release

Pull Request - State: closed - Opened by MuhammedHasan almost 5 years ago
Labels: bug

#33 - Breaks with latest versions of kipoiseq

Issue - State: closed - Opened by aerval almost 5 years ago - 1 comment
Labels: bug

#32 - writeVCF not implemented. I wrote some implementation

Issue - State: closed - Opened by beskns about 5 years ago - 6 comments
Labels: question

#31 - Please set keras<=2.2.5 in requirements. Not work with keras=2.3

Issue - State: closed - Opened by beskns about 5 years ago - 1 comment
Labels: bug

#30 - Can MMSplice be used for mouse or other non-human organisms?

Issue - State: closed - Opened by xinghua1001 about 5 years ago - 1 comment
Labels: duplicate, question

#29 - Variants without predictions

Issue - State: closed - Opened by dmb107 about 5 years ago - 1 comment
Labels: question

#28 - FAILED to annotate in VEP

Issue - State: closed - Opened by loganylchen about 5 years ago - 3 comments
Labels: question

#27 - Add performance test

Issue - State: closed - Opened by s6juncheng about 5 years ago - 1 comment
Labels: enhancement

#26 - Error when split_seq=False in dataloader

Issue - State: closed - Opened by s6juncheng about 5 years ago
Labels: enhancement

#25 - Exon dataloader

Pull Request - State: closed - Opened by MuhammedHasan about 5 years ago - 1 comment
Labels: enhancement

#24 - Exon module mask

Pull Request - State: closed - Opened by s6juncheng about 5 years ago

#23 - MTSplice

Pull Request - State: closed - Opened by MuhammedHasan about 5 years ago
Labels: enhancement

#22 - MMSplice output has only 5 columns

Issue - State: closed - Opened by Nairobi-2020 about 5 years ago

#21 - Running multiple jobs simultaneously

Issue - State: closed - Opened by Nairobi-2020 about 5 years ago

#20 - more vep plugin testing and fix for missing argument #19

Pull Request - State: closed - Opened by MuhammedHasan about 5 years ago
Labels: bug

#19 - VEP plugin with PYTHON error

Issue - State: closed - Opened by loganylchen about 5 years ago - 4 comments
Labels: bug

#18 - pyranges.df is an expensive operation, best to avoid?

Issue - State: closed - Opened by endrebak about 5 years ago - 2 comments
Labels: enhancement

#17 - Re-implement `exon_dataloader`

Issue - State: closed - Opened by MuhammedHasan about 5 years ago
Labels: enhancement

#15 - check_chrom_annotation

Issue - State: closed - Opened by MuhammedHasan about 5 years ago
Labels: enhancement

#14 - 0.2.8

Pull Request - State: closed - Opened by MuhammedHasan about 5 years ago - 1 comment

#13 - mmsplice couldn't output separate score of each kind of splice type

Issue - State: closed - Opened by zofieLin over 5 years ago - 2 comments

#12 - Ship mmsplice with prebuild exon set.

Issue - State: closed - Opened by MuhammedHasan over 5 years ago
Labels: enhancement

#11 - Refactor mmsplice with `kipoiseq` and `pyranges`

Issue - State: closed - Opened by MuhammedHasan over 5 years ago
Labels: enhancement

#10 - Error while installing mmsplice

Issue - State: closed - Opened by herrroaa over 5 years ago - 13 comments

#9 - version 0.2.8

Pull Request - State: closed - Opened by MuhammedHasan over 5 years ago

#8 - VEP plugin writes Tensorflow startup messages to stdout

Issue - State: closed - Opened by aerval over 5 years ago - 1 comment

#7 - version fixes

Pull Request - State: closed - Opened by MuhammedHasan over 5 years ago

#6 - VEP docker added and circle-ci testing for VEP plugin

Pull Request - State: closed - Opened by MuhammedHasan almost 6 years ago

#4 - WIP: Add docker file

Pull Request - State: closed - Opened by MuhammedHasan almost 6 years ago

#3 - Update config.yml

Pull Request - State: closed - Opened by s6juncheng almost 6 years ago

#2 - MMSplice on non-human VCF files

Issue - State: closed - Opened by vidhyajagannathan almost 6 years ago - 1 comment

#1 - vep plugin error

Issue - State: closed - Opened by yipukangda almost 6 years ago - 18 comments