@johnlees johnlees released this Jun 20, 2017 · 15 commits to master since this release

Assets 4

This includes gzstream as a submodule, and will be the version released under bioconda

Assets 5

This release adds the following features and fixes

  • Adds the likelihood ratio test (LRT) as the default p-value for binary traits (issue #42). This has higher power when effect sizes are large.
  • Ensure consistency of sample order when using mash rather than kmds. Previous releases will have assumed mash ordering was the same as seer; the .samples file is written correctly by the perl script and mitigates this.
  • Fix for the t-test in continuous traits, which could give incorrect p-values for negative effect sizes (issue #46).
  • Check for header with filter_seer and map_back

If using mash rather than kmds, please use this release or later.

@johnlees johnlees released this Oct 3, 2016 · 42 commits to master since this release

Assets 5

Adds

  • Replaces kmds with mash (but kmds still possible)
  • Normalise k-mer distances (as in manuscript)
  • New R script functionality plotting (issue #18)
  • Fixes issues #28, #29, #30, #32, #33, #34
  • map_back and filter_seer updated and bugs fixed
  • Add travis-ci

The features are as in the published manuscript, or higher

@johnlees johnlees released this Apr 11, 2016 · 91 commits to master since this release

Assets 5

Adds:

  • unit tests
  • information about covariates
  • invokes Firth regression more often
  • doesn't die on failed matrix inversions
  • checks for consistency of sample names
  • update and addition of some helper scripts

@johnlees johnlees released this Nov 18, 2015 · 114 commits to master since this release

Assets 4

Fixes bug in v1.0.1 where .pheno file was assumed to be sorted. Do not use previous releases, but see v1.0.1 for more release notes

@johnlees johnlees released this Nov 5, 2015 · 118 commits to master since this release

Assets 2

Compile instructions are in README.md. Other information (usage, troubleshooting) is in the wiki

Additions from v1.0.0

  • Faster with continuous phenotypes
  • map_back and filter_seer consistent with output
  • General clean up

Pre-compiled binaries for linux_64 are provided. Use the dynamic version with gcc-4.9 or above, and the dependencies installed. If this isn't possible, use the static version

Pre-release

@johnlees johnlees released this Oct 30, 2015 · 122 commits to master since this release

Assets 4

First version of seer. Instructions to compile are at the start of README.md, and usage follows

Pre-compiled binaries for linux_64 are provided. Use the dynamic version with gcc-4.9 or above, and the dependencies installed. If this isn't possible, use the static version