murphycj/AGFusion issues and pull requests

#55 - Bump black from 22.10.0 to 24.3.0

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#54 - Certificate expired on www.agfusion.app

Issue - State: closed - Opened by roland-ewald 10 months ago - 2 comments

#53 - can we use AGFusion for annotating gene fusions detected in plant?

Issue - State: open - Opened by Fiza250 about 1 year ago

#52 - Using agfusion build command for ensembl >v95?

Issue - State: open - Opened by min-codes over 1 year ago - 4 comments

#51 - Add docker

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

#50 - Fix Fusioninspector parser

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

#49 - Can I use the input from FusionInspector.

Issue - State: closed - Opened by WangKang-Leo over 1 year ago - 4 comments
Labels: bug

#48 - Support for LongGF

Pull Request - State: closed - Opened by murphycj almost 2 years ago

#47 - Add parser for arriba

Pull Request - State: closed - Opened by murphycj almost 2 years ago

#46 - Enhancement/38 star fusion input

Pull Request - State: closed - Opened by murphycj almost 2 years ago

#45 - Fix bug in plotting

Pull Request - State: closed - Opened by murphycj almost 2 years ago - 2 comments
Labels: bug

#44 - Issues with agfusion batch: TypeError: save_images() got an unexpected keyword argument 'plot_WT'

Issue - State: closed - Opened by QianhuiXu almost 2 years ago - 1 comment
Labels: bug

#43 - Add CI/CD, code formatting, and fix tests.

Pull Request - State: closed - Opened by murphycj almost 2 years ago

#42 - Please note that I do not actively maintain this repo anymore

Issue - State: closed - Opened by murphycj over 2 years ago

#41 - Add support for STAR-Fusion 1.10

Pull Request - State: closed - Opened by susannasiebert over 2 years ago - 1 comment

#40 - Bio.Alphabet has been removed from Biopython.

Issue - State: closed - Opened by fizwit about 3 years ago - 1 comment
Labels: bug

#39 - support for LongGF (new fusion finder for long read sequences)

Issue - State: closed - Opened by parsboy66 about 3 years ago

#38 - STAR-Fusion input

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

#37 - Support for arriba

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

#36 - Build database for Ensembl 100

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

#35 - Pyensembl Version

Issue - State: closed - Opened by hessmaria about 4 years ago

#34 - 5' UTR sequence not included when 3' gene junction is in 5' UTR

Issue - State: open - Opened by murphycj over 4 years ago
Labels: bug

#33 - issue for running agfusion

Issue - State: closed - Opened by kat-yuan over 4 years ago

#32 - Potential dependency conflicts between agfusion and numpy

Issue - State: closed - Opened by NeolithEra almost 5 years ago - 1 comment

#31 - Failing on gene names containing '/'

Issue - State: closed - Opened by stsergbg about 5 years ago - 1 comment

#30 - Frame issues

Issue - State: open - Opened by komalsrathi about 5 years ago - 4 comments

#29 - Unable to download database(agfusion.homo_sapiens.94.db)

Issue - State: closed - Opened by ShahiRB about 5 years ago - 2 comments

#28 - Frameshift fusions warning

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

#27 - Ensembl 96 support

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

#26 - Add gene direction to the exons output file

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

#25 - Unsupported species for H.sapiens ensembl 92

Issue - State: closed - Opened by zlskidmore over 5 years ago - 3 comments

#24 - Saving plots as pdf files

Issue - State: closed - Opened by msquatrito almost 6 years ago - 2 comments

#23 - rename and type not working

Issue - State: closed - Opened by msquatrito about 6 years ago - 5 comments

#22 - what file is used for infusion algorithm?

Issue - State: closed - Opened by foxchase about 6 years ago - 2 comments

#21 - missing domain in output?

Issue - State: closed - Opened by ghost over 6 years ago - 8 comments

#20 - using annotate --WT option causes exception

Issue - State: closed - Opened by ghost over 6 years ago - 4 comments

#19 - Strange behavior calling fusion frame

Issue - State: closed - Opened by juferban over 6 years ago - 1 comment

#18 - Documention

Issue - State: closed - Opened by ahgillmo over 6 years ago - 3 comments

#17 - Can This tool used for DNAseq?

Issue - State: closed - Opened by haoziyeung over 6 years ago - 2 comments

#16 - please tag releases

Issue - State: closed - Opened by 0xaf1f about 7 years ago - 1 comment

#15 - issue with batch

Issue - State: closed - Opened by kac2053 about 7 years ago - 6 comments

#14 - trouble getting agfusion.homo_sapiens.87.db to work with AGFusion

Issue - State: closed - Opened by kac2053 about 7 years ago - 11 comments
Labels: bug

#13 - TypeError: iter() returned non-iterator of type

Issue - State: closed - Opened by StevenIg about 7 years ago - 4 comments
Labels: bug

#12 - Include exon number

Issue - State: open - Opened by murphycj about 7 years ago - 1 comment
Labels: enhancement

#11 - Error plotting WT protein

Issue - State: closed - Opened by murphycj about 7 years ago
Labels: bug

#10 - Remove .bak

Pull Request - State: closed - Opened by ralic over 7 years ago

#9 - Convert to Python3

Pull Request - State: closed - Opened by ralic over 7 years ago

#8 - Not able to see protein domain information

Issue - State: closed - Opened by Nitin123-4 over 7 years ago - 3 comments
Labels: bug

#7 - Plot wild-type proteins

Issue - State: closed - Opened by murphycj over 7 years ago
Labels: enhancement

#6 - Ensembl perl db build

Pull Request - State: closed - Opened by murphycj over 7 years ago

#5 - Support RefSeq IDs

Issue - State: closed - Opened by murphycj almost 8 years ago - 1 comment
Labels: enhancement

#4 - Include all types of Ensembl domain annotations

Issue - State: closed - Opened by murphycj almost 8 years ago
Labels: enhancement

#3 - Images not created for GRCh37

Issue - State: closed - Opened by rhshah almost 8 years ago - 3 comments
Labels: bug

#2 - Overlapping text

Issue - State: closed - Opened by murphycj almost 8 years ago
Labels: bug, enhancement

#1 - HTML output and downloaded figure on web version have different font size or size

Issue - State: closed - Opened by murphycj almost 8 years ago
Labels: bug

GitHub / murphycj/AGFusion issues and pull requests