Ecosyste.ms: Issues

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

GitHub / czbiohub/cerebra issues and pull requests

#112 - Bump setuptools from 47.3.1 to 65.5.1

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

#111 - Bump numpy from 1.18.1 to 1.22.0

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

#110 - count-variants not runnable without specifying cosmicdb

Issue - State: open - Opened by lincoln-harris over 3 years ago - 1 comment

#109 - JOSS review comments -- redux

Pull Request - State: closed - Opened by lincoln-harris about 4 years ago - 1 comment

#108 - JoSS Review: Community Guidelines

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

#107 - JoSS Review: Automated Tests

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

#106 - JoSS Review: Functionality

Issue - State: closed - Opened by betteridiot about 4 years ago - 3 comments

#105 - JoSS Review: Installation

Issue - State: closed - Opened by betteridiot about 4 years ago - 5 comments

#104 - reformatted docs

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#103 - vcfpy exception

Issue - State: closed - Opened by lincoln-harris over 4 years ago - 2 comments
Labels: bug

#102 - merging `mito-checkout` into master

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 4 comments

#101 - zlib error

Issue - State: closed - Opened by lincoln-harris over 4 years ago - 2 comments
Labels: bug

#100 - some adnl improvements on the testing front

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#99 - hgvs throwing stdout

Issue - State: closed - Opened by lincoln-harris over 4 years ago

#98 - various

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

#97 - would like to make cerebra modules importable

Issue - State: closed - Opened by lincoln-harris over 4 years ago

#96 - appeasing codecov bot

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

#95 - stupid merge -- forgot to switch back to master

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

#94 - merging pytest-sandbox with master

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago
Labels: enhancement

#93 - adding in Dockerfile

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

#92 - trouble adding to bioconda

Issue - State: open - Opened by lincoln-harris over 4 years ago

#91 - really stupid PR -- forgot to switch back to master

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

#90 - JoSS Review: Quality of writing

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

#89 - JoSS Review: Clarify README.md

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

#88 - merge windows-ci branch into master

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#87 - Py3.8 sandbox into master

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 3 comments

#86 - pysam build fails on python3.8

Issue - State: open - Opened by lincoln-harris over 4 years ago - 5 comments

#85 - improve testing speed

Issue - State: closed - Opened by lincoln-harris over 4 years ago - 3 comments

#84 - merging JOSS-review branch into master

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 5 comments

#83 - Installation process

Issue - State: closed - Opened by afrubin over 4 years ago - 8 comments

#82 - Review comments on CONTRIBUTING.md

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

#81 - Universal wheel

Issue - State: closed - Opened by afrubin over 4 years ago

#80 - Python 3.8 support

Issue - State: closed - Opened by afrubin over 4 years ago

#79 - Requirements and CI

Issue - State: closed - Opened by afrubin over 4 years ago

#78 - Versioning question

Issue - State: closed - Opened by afrubin over 4 years ago

#77 - integrating comments from SD and OBB

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#76 - More paper edits

Pull Request - State: closed - Opened by olgabot over 4 years ago - 5 comments

#75 - integrating in spyros' comments

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 2 comments

#74 - renamed cmdline args in germline-filter, along with various changes to README

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#73 - merging personal fork into main repository

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#72 - merging various paper.md changes in master

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

#71 - consider changing mutations -> variants in module names

Issue - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#70 - add prebuilt index for genome.fa

Issue - State: open - Opened by lincoln-harris over 4 years ago - 2 comments
Labels: enhancement, wontfix

#69 - started reformatting

Pull Request - State: closed - Opened by olgabot over 4 years ago - 3 comments

#68 - test dir reorganization

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 2 comments

#67 - make germline-filter module more robust

Issue - State: open - Opened by lincoln-harris over 4 years ago - 2 comments
Labels: enhancement

#66 - add comprehensive test for germline_filter

Issue - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#65 - filtered_cosmic_db in count_mutations.py limiting to lung

Issue - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment
Labels: bug

#64 - turned off _make_filtered_cosmic_df

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#63 - filtered_cosmic_db in find_aa_mutations limiting to lung

Issue - State: closed - Opened by lincoln-harris over 4 years ago
Labels: bug

#62 - adding a couple of tests

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#61 - should have done this before i started adding tests

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

#60 - Travis patch

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#59 - wierd Bioseq install error -- package not found

Issue - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#58 - Update setup.py

Pull Request - State: closed - Opened by olgabot over 4 years ago - 1 comment

#57 - merging paper.md branch

Pull Request - State: closed - Opened by lincoln-harris over 4 years ago - 1 comment

#56 - Patch for mito wierdness

Pull Request - State: closed - Opened by lincoln-harris almost 5 years ago - 1 comment

#55 - patch fix for race condition

Pull Request - State: closed - Opened by lincoln-harris almost 5 years ago - 2 comments

#54 - JOSS guidelines

Issue - State: closed - Opened by lincoln-harris almost 5 years ago

#53 - germline-filter run instructions

Issue - State: closed - Opened by not-rs almost 5 years ago - 5 comments
Labels: enhancement, question

#52 - clarification on AD field of vcf files

Issue - State: closed - Opened by lincoln-harris almost 5 years ago - 2 comments
Labels: question

#51 - setup docker container

Issue - State: closed - Opened by lincoln-harris almost 5 years ago - 2 comments
Labels: enhancement

#50 - added process lock

Pull Request - State: closed - Opened by lincoln-harris almost 5 years ago - 2 comments

#49 - Reformatted code with pep8

Pull Request - State: closed - Opened by lincoln-harris almost 5 years ago - 1 comment

#48 - output json instead of csv

Issue - State: closed - Opened by lincoln-harris almost 5 years ago - 2 comments
Labels: enhancement

#47 - multiprocessing race condition

Issue - State: closed - Opened by lincoln-harris almost 5 years ago - 10 comments
Labels: bug, help wanted

#46 - adding test_mutation_counts changes

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

#45 - Draft PR -- build passing!!

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

#44 - testing travis

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

#43 - Adding env yaml

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

#42 - merge get_coverage_refactor branch into aa-mutations-working

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

#41 - find-aa-mutations not working, post-merge with Rohan's branch

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

#40 - AA mutations working merge w/master

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

#39 - AA mutations

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

#38 - Mutation counts cleanup

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

#37 - what is the status of dev?

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

#36 - Supporting different types of annotation GTFs

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

#35 - removing germline_filter module

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

#34 - PR on mutation_counts module

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

#33 - Revert "merge genomeIntervalTree-test-case > master"

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

#32 - merge genomeIntervalTree-test-case > master

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

#31 - Revert "merging genomeIntervalTree-test-case into dev"

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

#30 - merging genomeIntervalTree-test-case into dev

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

#29 - add travis-ci badge

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

#27 - need to integrate gvcf search into coverage module

Issue - State: closed - Opened by lincoln-harris over 5 years ago

#26 - GenomePosition.from_str shouldn't assume 1-index

Issue - State: open - Opened by rvanheusden over 5 years ago

#25 - vcf '20' field is sometimes malformed

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

#24 - improve germline filtering: handle multiple ALTs better

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

#22 - perhaps give non-tumor cells better names for germline filtering

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

#21 - add dbSNP filter, probably in germline_filter.py module

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

#19 - need to integrate coverage module

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

#18 - not picking up intronic variants

Issue - State: open - Opened by lincoln-harris over 5 years ago
Labels: enhancement

#9 - fathmm filter excludes a bunch of indels

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

#5 - mapping ambiguity between vcf and gtf

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

#4 - how to deal with vcf records with multiple *ALT*s?

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