Ecosyste.ms: Issues

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

GitHub / hammerlab/variant-calling-benchmarks issues and pull requests

#41 - Generate data with Mitty?

Issue - State: open - Opened by hammer over 8 years ago

#41 - Generate data with Mitty?

Issue - State: open - Opened by hammer over 8 years ago

#40 - Seraseq™ Solid Tumor Mutation Mix

Issue - State: open - Opened by hammer over 8 years ago

#40 - Seraseq™ Solid Tumor Mutation Mix

Issue - State: open - Opened by hammer over 8 years ago

#39 - A somatic reference standard for cancer genome sequencing

Issue - State: open - Opened by arahuja over 8 years ago

#39 - A somatic reference standard for cancer genome sequencing

Issue - State: open - Opened by arahuja over 8 years ago

#38 - SKBR3 PacBio Sequencing

Issue - State: open - Opened by hammer over 8 years ago - 1 comment
Labels: somatic dataset

#38 - SKBR3 PacBio Sequencing

Issue - State: open - Opened by hammer over 8 years ago - 1 comment
Labels: somatic dataset

#37 - Texas Cancer Research Biobank (TCRB) data

Issue - State: open - Opened by hammer over 8 years ago
Labels: somatic dataset

#37 - Texas Cancer Research Biobank (TCRB) data

Issue - State: open - Opened by hammer over 8 years ago
Labels: somatic dataset

#36 - Mutect calls for dream

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#36 - Mutect calls for dream

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#35 - Add pt189

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#35 - Add pt189

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#34 - Fixes

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#34 - Fixes

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#33 - Support for submitting results to google cloud bucket

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#33 - Support for submitting results to google cloud bucket

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#31 - Better configuration system, configurable `spark-submit` and env vars

Pull Request - State: closed - Opened by timodonnell over 8 years ago - 2 comments

#31 - Better configuration system, configurable `spark-submit` and env vars

Pull Request - State: closed - Opened by timodonnell over 8 years ago - 2 comments

#30 - Add instructions for syncing results to google cloud bucket

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#30 - Add instructions for syncing results to google cloud bucket

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#29 - bzip2 compress result VCF and CSVs

Issue - State: closed - Opened by timodonnell over 8 years ago

#29 - bzip2 compress result VCF and CSVs

Issue - State: closed - Opened by timodonnell over 8 years ago

#28 - Support running benchmarks on mutect + strelka

Issue - State: open - Opened by timodonnell over 8 years ago - 5 comments

#28 - Support running benchmarks on mutect + strelka

Issue - State: open - Opened by timodonnell over 8 years ago - 5 comments

#27 - num-executors in demeter.json

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

#27 - num-executors in demeter.json

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

#26 - Add DREAM synth1 benchmark and variants from VCF

Pull Request - State: closed - Opened by arahuja over 8 years ago - 2 comments

#26 - Add DREAM synth1 benchmark and variants from VCF

Pull Request - State: closed - Opened by arahuja over 8 years ago - 2 comments

#25 - Remove duplicate argument

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#25 - Remove duplicate argument

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#24 - consider better ways of specifying guacamole jars

Issue - State: open - Opened by timodonnell over 8 years ago

#24 - consider better ways of specifying guacamole jars

Issue - State: open - Opened by timodonnell over 8 years ago

#23 - Fix local run to use guacamole dependencies jar

Pull Request - State: closed - Opened by timodonnell over 8 years ago - 1 comment

#23 - Fix local run to use guacamole dependencies jar

Pull Request - State: closed - Opened by timodonnell over 8 years ago - 1 comment

#22 - local run example is wrong, uses outdated guacamole-with-dependencies jar

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

#22 - local run example is wrong, uses outdated guacamole-with-dependencies jar

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

#21 - setup a nightly run

Issue - State: open - Opened by timodonnell over 8 years ago - 2 comments

#21 - setup a nightly run

Issue - State: open - Opened by timodonnell over 8 years ago - 2 comments

#20 - figure out how to test, setup travis and coveralls

Issue - State: open - Opened by timodonnell over 8 years ago

#20 - figure out how to test, setup travis and coveralls

Issue - State: open - Opened by timodonnell over 8 years ago

#19 - First cut on vcb-guacamole-cluster script

Pull Request - State: closed - Opened by timodonnell over 8 years ago - 1 comment

#19 - First cut on vcb-guacamole-cluster script

Pull Request - State: closed - Opened by timodonnell over 8 years ago - 1 comment

#18 - specificity computation

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

#18 - specificity computation

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

#17 - Document benchmark.json

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

#17 - Document benchmark.json

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

#16 - Add PT189 benchmark

Issue - State: open - Opened by timodonnell over 8 years ago
Labels: somatic dataset

#16 - Add PT189 benchmark

Issue - State: open - Opened by timodonnell over 8 years ago
Labels: somatic dataset

#15 - create results directory

Pull Request - State: closed - Opened by arahuja over 8 years ago - 1 comment

#15 - create results directory

Pull Request - State: closed - Opened by arahuja over 8 years ago - 1 comment

#14 - Fix local-wgs1 benchmark

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#14 - Fix local-wgs1 benchmark

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#13 - no good calls in local-wgs1 benchmark

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

#13 - no good calls in local-wgs1 benchmark

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

#12 - support running on google cloud

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

#12 - support running on google cloud

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

#11 - support running on demeter

Issue - State: closed - Opened by timodonnell over 8 years ago

#11 - support running on demeter

Issue - State: closed - Opened by timodonnell over 8 years ago

#10 - First cut

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#10 - First cut

Pull Request - State: closed - Opened by timodonnell over 8 years ago

#9 - PANCREATIC CANCER - AU

Issue - State: open - Opened by arahuja over 8 years ago
Labels: somatic dataset

#9 - PANCREATIC CANCER - AU

Issue - State: open - Opened by arahuja over 8 years ago
Labels: somatic dataset

#7 - Add DREAM synthetic data

Issue - State: open - Opened by timodonnell over 8 years ago
Labels: somatic dataset

#7 - Add DREAM synthetic data

Issue - State: open - Opened by timodonnell over 8 years ago
Labels: somatic dataset

#6 - add updated Illumina platnium dataset of high quality germline calls

Issue - State: open - Opened by timodonnell over 8 years ago
Labels: germline dataset

#6 - add updated Illumina platnium dataset of high quality germline calls

Issue - State: open - Opened by timodonnell over 8 years ago
Labels: germline dataset

#5 - Download AML31 data from "Optimizing Cancer Genome Sequencing and Analysis"

Issue - State: open - Opened by timodonnell over 8 years ago - 15 comments
Labels: somatic dataset

#5 - Download AML31 data from "Optimizing Cancer Genome Sequencing and Analysis"

Issue - State: open - Opened by timodonnell over 8 years ago - 15 comments
Labels: somatic dataset

#3 - Add TCGA samples with validated variants

Issue - State: open - Opened by timodonnell over 8 years ago
Labels: somatic dataset

#3 - Add TCGA samples with validated variants

Issue - State: open - Opened by timodonnell over 8 years ago
Labels: somatic dataset

#2 - Add checkpoint trials data where there is IMPACT or other panel

Issue - State: open - Opened by timodonnell over 8 years ago
Labels: somatic dataset

#1 - Add AOCS patient 034 to establish data schema and workflow

Issue - State: closed - Opened by timodonnell over 8 years ago - 1 comment
Labels: somatic dataset