Brent Pedersen - Bioinformatics
- University of Utah
- Salt Lake City, UT
- Joined on
- bio-playground 82 miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
- cruzdb 64 python access to UCSC genomes database
- pyfasta 43 fast, memory-efficient, pythonic (and command-line) access to fasta sequence files
- vcfanno 40 annotate a VCF with other VCFs/BEDs/tabixed files
- xopen 30 open files for buffered reading and writing in #golang
Repositories contributed to
- arq5x/gemini 138 a lightweight db framework for disease and population genetics.
- bioconda/bioconda-recipes 60 Conda recipes for the bioconda channel.
- jimhavrilla/pmodel 3 For modeling genetic variation based on protein domains
- ryanlayer/ssshtest 7 Stupid Simple (ba)Sh Testing - A functional software testing framwork
- arq5x/cyvcf 24 A fast Python library for VCF files leveraging Cython for speed.
Contributions in the last year 1,955 total Feb 6, 2015 – Feb 6, 2016
Longest streak 33 days April 20 – May 22
Current streak 4 days February 2 – February 5
- Pushed 4 commits to bioconda/bioconda-recipes Feb 3 – Feb 5
- Pushed 11 commits to jimhavrilla/pmodel Feb 5
- Pushed 21 commits to arq5x/ggd Feb 4 – Feb 5
- Pushed 5 commits to brentp/ggd-hg38-recipes Feb 4
- Pushed 11 commits to arq5x/gemini Feb 2 – Feb 4
11 Pull Requests
- Merged #758 bump gemini to 0.18.1
- Merged #21 only copy files from a recipe when all of the sections have completed…
- Merged #20 add tests. closes #18.
- Merged #19 set non-zero exit codes on errors. closes #14.
- Merged #13 convert to 4 space indent. install yaml script
- Merged #670 update tests that changed becuase of variant prioritization
- Merged #746 bump geneimpacts
- Merged #668 stub in inheritance module to get GeminiQuery autodoc
- Merged #667 don't import gemini to get version. fixes problems with docs
- Merged #666 Docsreqs
- Merged #665 fix bug in mendel_errors tool. Closes #664.
10 Issues reported
- Closed #23 template variables
- Open #22 make and get sections
- Closed #18 recipe responsible for writing files
- Open #17 dependencies on other recipes and on softare
- Open #16 versioning
- Open #15 allow simpler running of installing single local yaml
- Closed #14 set exit codes on errors.
- Open #669 ExAC not getting update for some people.
- Closed #22 GQ should be Type=Integer
- Open #663 allow using canonical transcript instead of highest impact