Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / bigbio/py-pgatk issues and pull requests
#83 - disable cbioportal download test
Pull Request -
State: closed - Opened by ypriverol 2 months ago
#81 - Spectrum ai
Pull Request -
State: closed - Opened by ypriverol 2 months ago
#80 - Spectrum ai
Pull Request -
State: closed - Opened by ypriverol 2 months ago
#79 - update new blast and spectrumAI
Pull Request -
State: closed - Opened by DongdongdongW 2 months ago
#78 - Minor bug fixed
Pull Request -
State: closed - Opened by ypriverol 2 months ago
#77 - spectrumAI into py-pgatk
Pull Request -
State: closed - Opened by ypriverol 3 months ago
#76 - update validate
Pull Request -
State: closed - Opened by DongdongdongW 3 months ago
#75 - Bump requests from 2.21.0 to 2.31.0
Pull Request -
State: closed - Opened by dependabot[bot] about 1 year ago
- 2 comments
Labels: dependencies
#74 - vcf-to-proteindb returned incorrect amino acid sequences
Issue -
State: open - Opened by AlirezaShokrollahi over 1 year ago
#73 - fixes issue #72
Pull Request -
State: closed - Opened by husensofteng over 1 year ago
#72 - Incompatible COSMIC mutation records
Issue -
State: open - Opened by husensofteng over 1 year ago
#71 - Fix the bug of class-fdr, adjust the blast to multi-process running t…
Pull Request -
State: closed - Opened by DongdongdongW over 1 year ago
#70 - add spectrumAI
Pull Request -
State: closed - Opened by DongdongdongW almost 2 years ago
- 8 comments
#69 - update
Pull Request -
State: closed - Opened by ypriverol almost 2 years ago
#68 - fixed bug in gtf file name, just keep version not release string
Pull Request -
State: closed - Opened by ypriverol almost 2 years ago
#67 - Improve test case to check download
Issue -
State: open - Opened by husensofteng almost 2 years ago
Labels: enhancement
#66 - change var_prefix
Issue -
State: closed - Opened by husensofteng almost 2 years ago
Labels: enhancement
#65 - implement spectrumAI in pypgatk
Issue -
State: closed - Opened by ypriverol about 2 years ago
- 3 comments
#64 - major changes dealing with configs files
Pull Request -
State: closed - Opened by ypriverol about 2 years ago
- 2 comments
#63 - Updates version info for
Pull Request -
State: closed - Opened by ypriverol about 2 years ago
#62 - changes in the generation for msrescore
Pull Request -
State: closed - Opened by ypriverol about 2 years ago
#61 - Write urls for download into file instead of downloading
Issue -
State: closed - Opened by ypriverol about 2 years ago
Labels: bug
#60 - changes to fix problem with config files
Pull Request -
State: closed - Opened by ypriverol about 2 years ago
#59 - gffread fasta generated file uses space and semicolon
Issue -
State: closed - Opened by husensofteng about 2 years ago
- 1 comment
Labels: enhancement
#58 - changing values in the config files have no effect
Issue -
State: closed - Opened by husensofteng about 2 years ago
Labels: bug
#57 - Updated vcf-to-proteindb to parse using pandas
Pull Request -
State: closed - Opened by husensofteng over 2 years ago
#56 - Implementation of Class FDR
Issue -
State: closed - Opened by ypriverol over 2 years ago
- 10 comments
Labels: enhancement
#55 - pyVCF reader deprecated only supported for py3.6
Issue -
State: closed - Opened by ypriverol over 2 years ago
Labels: bug
#54 - Class FDR (Please do not merge, this yet)
Pull Request -
State: closed - Opened by ypriverol over 2 years ago
- 3 comments
Labels: bug, enhancement
#53 - reports error when ref/alt alleles are not set to nucleotides ACGT in…
Pull Request -
State: closed - Opened by husensofteng over 2 years ago
#52 - Error: Codon '-CT' is invalid
Issue -
State: closed - Opened by enriquea over 2 years ago
- 8 comments
#50 - Cleaning the code
Issue -
State: closed - Opened by ypriverol over 2 years ago
- 1 comment
Labels: enhancement
#49 - Update the urlib library
Pull Request -
State: closed - Opened by ypriverol over 2 years ago
- 1 comment
#48 - Generating protein DB from custom VCF fails
Issue -
State: closed - Opened by enriquea over 2 years ago
- 4 comments
#47 - wrong cosmic proteins output
Issue -
State: closed - Opened by GeorgesBed almost 3 years ago
- 6 comments
#46 - Bump urllib3 from 1.24.2 to 1.26.5
Pull Request -
State: closed - Opened by dependabot[bot] about 3 years ago
- 1 comment
Labels: dependencies
#45 - Dev
Pull Request -
State: closed - Opened by husensofteng over 3 years ago
#44 - Dev
Pull Request -
State: closed - Opened by husensofteng over 3 years ago
- 1 comment
#43 - Bump pyyaml from 5.1 to 5.4
Pull Request -
State: closed - Opened by dependabot[bot] over 3 years ago
- 1 comment
Labels: dependencies
#42 - Dev
Pull Request -
State: closed - Opened by husensofteng over 3 years ago
#41 - Major changes
Pull Request -
State: closed - Opened by ypriverol over 3 years ago
#40 - Merge pull request #39 from bigbio/dev
Pull Request -
State: closed - Opened by ypriverol over 3 years ago
#38 - Dev
Pull Request -
State: closed - Opened by husensofteng over 3 years ago
#37 - Dev
Pull Request -
State: closed - Opened by husensofteng over 3 years ago
- 1 comment
#36 - Clean code style
Pull Request -
State: closed - Opened by ypriverol over 3 years ago
#34 - Bump cryptography from 3.2 to 3.3.2
Pull Request -
State: closed - Opened by dependabot[bot] over 3 years ago
- 1 comment
Labels: dependencies
#32 - Change translation to generate all protein sequences
Pull Request -
State: closed - Opened by husensofteng over 3 years ago
#31 - handle the stop codons, COSMIC errors download, ENSEMBL releases
Pull Request -
State: closed - Opened by ypriverol over 3 years ago
- 3 comments
#30 - Errors and tasks to be implemented
Issue -
State: closed - Opened by ypriverol over 3 years ago
- 1 comment
#29 - Fasta input for vcf-to-proteindb
Issue -
State: closed - Opened by OmerRonen over 3 years ago
- 8 comments
Labels: help wanted
#28 - Cosmic mutations for celllines
Issue -
State: closed - Opened by ypriverol over 3 years ago
- 1 comment
Labels: enhancement
#27 - Bump cryptography from 2.6.1 to 3.2
Pull Request -
State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies
#26 - replace --list_taxonomies with list_names
Issue -
State: closed - Opened by husensofteng almost 5 years ago
- 2 comments
#25 - Error from ENSEMBL URL retry
Issue -
State: closed - Opened by ypriverol almost 5 years ago
Labels: bug
#24 - NCBI GTF/GFF - support for clinvar VCF
Issue -
State: open - Opened by husensofteng almost 5 years ago
Labels: enhancement
#23 - Ensembl release
Issue -
State: closed - Opened by husensofteng almost 5 years ago
Labels: enhancement
#22 - Add a changelog.md to the project
Issue -
State: closed - Opened by ypriverol almost 5 years ago
Labels: enhancement
#21 - Adding a converter for PEFF
Issue -
State: open - Opened by ypriverol about 5 years ago
- 1 comment
Labels: enhancement
#20 - Downloading all the cBioPortal experiments failing
Issue -
State: closed - Opened by ypriverol about 5 years ago
- 7 comments
Labels: bug
#19 - Add the decoy Sanger tool to the library
Issue -
State: closed - Opened by ypriverol about 5 years ago
- 16 comments
Labels: enhancement
#18 - Header of the proteins for search engines
Issue -
State: open - Opened by ypriverol about 5 years ago
Labels: enhancement
#17 - overlap between config parameters in cgenomes between cosmic and cbioportal downloaders
Issue -
State: closed - Opened by husensofteng about 5 years ago
- 4 comments
Labels: enhancement, help wanted
#16 - Documentation improvement
Issue -
State: open - Opened by ypriverol about 5 years ago
- 4 comments
#15 - Web application containing all databases and urls to be download
Issue -
State: closed - Opened by ypriverol about 5 years ago
#14 - Create a Nextflow workflow to create custom databases
Issue -
State: closed - Opened by ypriverol about 5 years ago
#13 - Major refactoring of the library to be more package oriented design
Issue -
State: closed - Opened by ypriverol about 5 years ago
- 1 comment
Labels: enhancement
#12 - move pepBedR to python.
Issue -
State: open - Opened by ypriverol about 5 years ago
Labels: enhancement
#11 - Download gnomAD variants and matching fasta
Issue -
State: closed - Opened by husensofteng about 5 years ago
- 1 comment
#10 - VCF to proteinDB
Issue -
State: closed - Opened by husensofteng about 5 years ago
- 2 comments
#9 - Download population variants from ENSEMBL
Issue -
State: closed - Opened by husensofteng about 5 years ago
- 11 comments
#8 - Major review to the code
Issue -
State: closed - Opened by ypriverol about 5 years ago
- 2 comments
Labels: enhancement, help wanted
#7 - Post-filter peptides
Issue -
State: closed - Opened by husensofteng about 5 years ago
- 1 comment
#6 - GTF to DNA seq
Issue -
State: closed - Opened by husensofteng about 5 years ago
#5 - ORFs to peptides
Issue -
State: closed - Opened by husensofteng about 5 years ago
#4 - DNA seq to ORFs:
Issue -
State: closed - Opened by husensofteng about 5 years ago
#3 - Alt ORFs from protein sequences
Issue -
State: closed - Opened by husensofteng about 5 years ago
- 1 comment
#2 - Download cancer studies from cbioportal
Issue -
State: closed - Opened by ypriverol about 5 years ago
#1 - Create / Download Canonical protein fasta file from ENSEMBL
Issue -
State: closed - Opened by ypriverol about 5 years ago
- 5 comments
Labels: enhancement