Ecosyste.ms: Issues

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

GitHub / hammerlab/cohorts issues and pull requests

#257 - Allow additional MAF columns

Pull Request - State: closed - Opened by tavinathanson about 7 years ago - 1 comment

#256 - Fix effects filtering for splice sites

Pull Request - State: closed - Opened by tavinathanson over 7 years ago - 2 comments

#254 - Fix effect priority caching

Pull Request - State: closed - Opened by tavinathanson over 7 years ago - 6 comments

#253 - all_effects caches, but does not return, all effects

Issue - State: closed - Opened by tavinathanson over 7 years ago - 1 comment
Labels: bug

#252 - Don't cache after only top-priority effects; post-filter instead

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

#251 - Refactor `_load_single_patient_variants` function

Issue - State: open - Opened by jburos over 7 years ago
Labels: enhancement

#250 - Test new parameters - fail_on_missing_bams, etc

Issue - State: open - Opened by jburos over 7 years ago
Labels: enhancement

#249 - Small fixes to improve estimation of expressed neoantigens

Pull Request - State: open - Opened by jburos over 7 years ago - 15 comments

#248 - Capture logger output when caching a result

Issue - State: open - Opened by jburos over 7 years ago
Labels: enhancement

#247 - KeyError when predicting neoantigens

Issue - State: open - Opened by jburos over 7 years ago

#246 - logging does not respond to user-configured level

Issue - State: open - Opened by jburos over 7 years ago

#245 - Report on but do not error when patient has no RNA data

Pull Request - State: open - Opened by jburos over 7 years ago - 15 comments

#244 - add get-blob method to gcio

Pull Request - State: closed - Opened by jburos over 7 years ago - 1 comment

#243 - Add indel effects

Pull Request - State: open - Opened by jburos over 7 years ago - 7 comments

#242 - add `join_on_left` parameter to dataframe_loader

Pull Request - State: closed - Opened by jburos over 7 years ago - 6 comments

#241 - Expose gcloud utils

Pull Request - State: closed - Opened by jburos over 7 years ago - 1 comment

#240 - plot_survival for the whole cohort, not "on" something

Issue - State: open - Opened by jburos over 7 years ago
Labels: enhancement

#239 - Set mhcflurry as the default MHC binding predictor

Issue - State: open - Opened by tavinathanson over 7 years ago
Labels: enhancement

#238 - Explain why predicted neoantigens are NaN when HLA types missing

Issue - State: open - Opened by jburos over 7 years ago
Labels: documentation

#237 - Plot surv by strata

Pull Request - State: closed - Opened by jburos over 7 years ago - 8 comments

#236 - allow median-vaf-purity with patients having no variants

Pull Request - State: closed - Opened by jburos over 7 years ago - 1 comment

#235 - Fix mhcnames to v 0.1.0

Pull Request - State: closed - Opened by jburos over 7 years ago - 2 comments

#234 - Update README & documentation to match current usage

Issue - State: open - Opened by jburos over 7 years ago
Labels: documentation

#233 - ImportError: cannot import name 'AlleleParseError'

Issue - State: closed - Opened by jburos over 7 years ago - 2 comments

#232 - "guess" at variant file format, if not obvious from filename

Pull Request - State: closed - Opened by jburos over 7 years ago - 2 comments

#231 - StopIteration error results in cached empty VariantCollection

Issue - State: open - Opened by tavinathanson over 7 years ago
Labels: bug

#230 - Update warning and associated comment

Pull Request - State: closed - Opened by tavinathanson over 7 years ago - 2 comments

#229 - Gcloud batch downloads

Pull Request - State: closed - Opened by jburos over 7 years ago - 3 comments

#228 - Error using median_vaf_purity on a combined-polyphen-snpeff.vcf

Issue - State: open - Opened by jburos over 7 years ago - 6 comments
Labels: bug

#227 - Help with creating a cohort

Issue - State: open - Opened by js2dark over 7 years ago - 14 comments

#226 - Make cohorts more workflow-engine and cloud storage friendly

Issue - State: open - Opened by armish over 7 years ago

#225 - Feature plot_survival by category (clean branch)

Pull Request - State: closed - Opened by jburos over 7 years ago - 3 comments

#224 - Feature - plot survival by category

Pull Request - State: closed - Opened by jburos over 7 years ago - 2 comments

#223 - Fix RGBA error with plot_survival

Pull Request - State: closed - Opened by jburos over 7 years ago - 2 comments

#222 - Warn on vcf errors

Pull Request - State: closed - Opened by jburos over 7 years ago - 14 comments

#221 - Invalid RGBA argument error using `plot_survival`

Issue - State: closed - Opened by jburos over 7 years ago - 3 comments

#219 - Google Storage file access add-on for cohorts (a.k.a. minibucket)

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

#218 - Support easy Cohort creation

Issue - State: open - Opened by tavinathanson over 7 years ago

#217 - support plotting survival curves for more than 2 groups

Issue - State: closed - Opened by jburos over 7 years ago - 1 comment

#216 - add cache_root_dir attribute & behavior

Pull Request - State: closed - Opened by jburos over 7 years ago - 3 comments

#215 - refactor caching (more robust API for caching functions)

Issue - State: closed - Opened by jburos over 7 years ago - 3 comments
Labels: duplicate

#214 - Add `cache_root_dir` attribute

Issue - State: closed - Opened by jburos over 7 years ago - 3 comments

#213 - small fix to address #212

Pull Request - State: closed - Opened by jburos over 7 years ago - 2 comments

#212 - median_vaf_purity() got an unexpected keyword argument 'normalized_per_mb'

Issue - State: closed - Opened by jburos over 7 years ago - 1 comment

#211 - Multi-sample API

Issue - State: open - Opened by tavinathanson over 7 years ago - 4 comments

#210 - Add new PyPi server

Pull Request - State: closed - Opened by tavinathanson over 7 years ago - 2 comments

#209 - Optionally Ketrew-ify cache generation?

Issue - State: open - Opened by tavinathanson over 7 years ago

#208 - Require Python 3

Pull Request - State: closed - Opened by tavinathanson over 7 years ago - 6 comments

#207 - progress reporting often prints multiple lines

Issue - State: open - Opened by jburos over 7 years ago - 2 comments
Labels: bug

#206 - Add optional show_progress

Pull Request - State: closed - Opened by tavinathanson over 7 years ago - 6 comments

#205 - Update Pageant logic

Pull Request - State: closed - Opened by tavinathanson over 7 years ago - 9 comments

#204 - Drop Python 2 support

Issue - State: closed - Opened by tavinathanson over 7 years ago - 2 comments

#203 - TypeError: "load_maf() got an unexpected keyword argument 'encoding'"

Issue - State: closed - Opened by jburos over 7 years ago - 9 comments

#202 - Cohorts does not work with latest mhctools

Issue - State: open - Opened by tavinathanson almost 8 years ago - 2 comments

#201 - Solve intermittent test failures

Issue - State: closed - Opened by tavinathanson almost 8 years ago - 1 comment

#200 - Add unit test for `require_id_str` to handle unicode

Issue - State: open - Opened by jburos almost 8 years ago

#199 - Update encoding and str handling for Py2/3 compatibility

Pull Request - State: closed - Opened by tavinathanson almost 8 years ago - 2 comments

#197 - Add patient __str__

Pull Request - State: closed - Opened by tavinathanson almost 8 years ago - 2 comments

#196 - Fixing filter cache issues

Pull Request - State: closed - Opened by tavinathanson almost 8 years ago - 6 comments

#195 - Not identifying filtered-cache-name in python 3

Issue - State: closed - Opened by jburos almost 8 years ago

#194 - Add support for ordinal `benefit` categories

Issue - State: open - Opened by jburos almost 8 years ago - 1 comment
Labels: enhancement

#193 - Don't allow PFS/OS values to be NaN?

Issue - State: closed - Opened by tavinathanson almost 8 years ago - 2 comments

#192 - Fix mhctools API integration

Issue - State: open - Opened by tavinathanson almost 8 years ago

#191 - Add frameshift count function

Issue - State: closed - Opened by tavinathanson almost 8 years ago

#189 - Add a median VAF filter function and a filter_fn watermark

Pull Request - State: closed - Opened by tavinathanson almost 8 years ago - 4 comments

#188 - Support stratified cohorts, as a way to combine more than one sample of patients

Issue - State: open - Opened by jburos almost 8 years ago - 1 comment

#187 - accomodate sampling weights

Issue - State: open - Opened by jburos almost 8 years ago

#186 - Refactor and fix functions

Pull Request - State: closed - Opened by tavinathanson almost 8 years ago - 5 comments

#185 - Do something with epidisco.py

Issue - State: open - Opened by tavinathanson almost 8 years ago - 1 comment
Labels: enhancement

#184 - Minor: old comment

Issue - State: closed - Opened by tavinathanson almost 8 years ago

#183 - Add watermark for default filter_fn on Cohort initialization

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

#182 - deletion_count is counting all indels

Issue - State: closed - Opened by tavinathanson almost 8 years ago - 1 comment
Labels: bug

#181 - exonic_silent_snv_count is confusing

Issue - State: closed - Opened by tavinathanson almost 8 years ago - 1 comment
Labels: bug

#180 - Add tests for VAF extraction from VCFs, BAMs

Issue - State: open - Opened by tavinathanson about 8 years ago
Labels: enhancement

#179 - Grab VAFs from MAFs

Pull Request - State: closed - Opened by tavinathanson about 8 years ago - 3 comments

#178 - Modify isovar usage from >=3 to >=2 spanning reads

Issue - State: open - Opened by tavinathanson about 8 years ago - 1 comment

#177 - Upgrade isovar to the latest version in cohorts

Pull Request - State: closed - Opened by tavinathanson about 8 years ago - 2 comments

#176 - Add isovar usage tests

Issue - State: open - Opened by tavinathanson about 8 years ago

#175 - Simplify cohorts caching

Issue - State: open - Opened by tavinathanson about 8 years ago - 2 comments

#174 - filter_fn result caching should work for Python 2 and 3

Issue - State: closed - Opened by tavinathanson about 8 years ago - 1 comment
Labels: bug

#173 - Number of functions is ballooning

Issue - State: closed - Opened by tavinathanson about 8 years ago - 1 comment

#172 - Pre-merge exonic counts into develop

Pull Request - State: closed - Opened by jburos about 8 years ago - 1 comment

#171 - Add exonic count functions

Pull Request - State: closed - Opened by jburos about 8 years ago - 2 comments

#170 - Cache sometimes fails if user interrupts writing process

Issue - State: closed - Opened by jburos about 8 years ago - 2 comments

#169 - Fix variant stats; cached filtered variants; add exonic counts; add progress bar

Pull Request - State: closed - Opened by jburos about 8 years ago - 14 comments

#168 - Fix variant stats

Pull Request - State: closed - Opened by jburos about 8 years ago

#167 - Support "merged" strelka VCF type

Issue - State: closed - Opened by jburos about 8 years ago - 2 comments

#166 - Using only Strelka tier 1 results in divide by zero sometimes

Issue - State: closed - Opened by tavinathanson about 8 years ago - 1 comment

#165 - Add more granular variant specification and other minor changes

Pull Request - State: closed - Opened by tavinathanson about 8 years ago - 7 comments

#164 - Random MHC prediction for random cohort

Pull Request - State: closed - Opened by tavinathanson about 8 years ago - 2 comments

#162 - Harmonize with epidisco

Issue - State: closed - Opened by hammer about 8 years ago - 2 comments
Labels: duplicate

#157 - kwargs does not work with single-function `on` dict

Issue - State: open - Opened by tavinathanson over 8 years ago - 1 comment

#155 - Write doc "Customizing filter functions"

Issue - State: open - Opened by jburos over 8 years ago
Labels: enhancement

#135 - Add capability to cache fitted Stan models [WIP]

Issue - State: open - Opened by jburos over 8 years ago - 1 comment
Labels: enhancement

#114 - Create public-facing usage template

Issue - State: closed - Opened by e5c over 8 years ago - 1 comment
Labels: enhancement

#69 - builds against latest versions of isovar fails

Issue - State: closed - Opened by jburos over 8 years ago - 1 comment