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

#82 - Dev

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

#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

#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

#52 - Error: Codon '-CT' is invalid

Issue - State: closed - Opened by enriquea over 2 years ago - 8 comments

#51 - Dev

Pull Request - State: closed - Opened by enriquea over 2 years ago

#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

#39 - 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

#35 - Dev

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

#33 - Dev

Pull Request - State: closed - Opened by ypriverol over 3 years ago

#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

#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