Pinned Repositories
2016-12-14-swcInsTest
2017-05-20-ucsf-r
2017-07-15-ucsf-r
alleleDB
The package includes the AlleleDB pipeline developed in the Gerstein Lab at Yale. This pipeline was built and applied to perform a uniform identification of SNVs associated with allele-specific binding and expression in 382 individuals from the 1000 Genomes Project. Please see website for more detailed README.
fratools
PERL scripts for managing genotype array data.
git-novice
Software Carpentry introduction to Git for novices.
health-analytics-ucsf
This is a repository for a seminar series conducted at UCSF in April 2017 by Prof. Arash Nourian.
immTransplant
Solid organ transplantation resource curated from clinical studies from the ImmPort database (http://www.immport.org/)
jmtools
This is a sandbox of scripts that I have created (~95%) or gathered from others since 2007. It is only stored here for utility and posterity. They are all constantly being updated, thus they should be treated as work-in-progress - raw and unpolished. Please ask for permission before publishing.
lesson-example
Example lesson using Software Carpentry template.
cjieming's Repositories
cjieming/2016-12-14-swcInsTest
cjieming/2017-05-20-ucsf-r
cjieming/2017-07-15-ucsf-r
cjieming/alleleDB
The package includes the AlleleDB pipeline developed in the Gerstein Lab at Yale. This pipeline was built and applied to perform a uniform identification of SNVs associated with allele-specific binding and expression in 382 individuals from the 1000 Genomes Project. Please see website for more detailed README.
cjieming/fratools
PERL scripts for managing genotype array data.
cjieming/git-novice
Software Carpentry introduction to Git for novices.
cjieming/health-analytics-ucsf
This is a repository for a seminar series conducted at UCSF in April 2017 by Prof. Arash Nourian.
cjieming/immTransplant
Solid organ transplantation resource curated from clinical studies from the ImmPort database (http://www.immport.org/)
cjieming/jmtools
This is a sandbox of scripts that I have created (~95%) or gathered from others since 2007. It is only stored here for utility and posterity. They are all constantly being updated, thus they should be treated as work-in-progress - raw and unpolished. Please ask for permission before publishing.
cjieming/lesson-example
Example lesson using Software Carpentry template.
cjieming/motifVar
The package includes the MotifVar pipeline developed in the Gerstein Lab at Yale for the Intensification resource. This pipeline was used to generate SNV population-genetic profiles using a variety of public data sources, including SMART domain database, ExAC, Ensembl and VEP. Please see website for more detailed README. This is a SEMI-automated pipeline, where possible manual work can be done on a small number of modules to make your analyses more accurate or specific to your needs. These modules are highlighted in the README and motifvar.sh wrapper with -m.
cjieming/R-ecology-lesson
:notebook: Data Carpentry R lessons on ecology. As of March 15, 2017 these lessons are frozen for significant changes in preparation for release.
cjieming/R_codes
This is a sandbox of scripts that I have created (~98%) or gathered from others since 2007. It is only stored here for utility and posterity. They are all constantly being updated, thus they should be treated as work-in-progress - raw and unpolished. Please ask for permission before publishing.
cjieming/shell-novice
Software Carpentry introduction to the shell for novices.
cjieming/varimedrisk
Scripts for running risk quantification using VARIMED and RiskOgram visualization in R