Ecosyste.ms: Issues

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GitHub / jbloomlab/phydms issues and pull requests

#46 - Tutorial typo fix

Pull Request - State: closed - Opened by gavinmdouglas 4 months ago

#45 - Typo in tutorial?

Issue - State: closed - Opened by gavinmdouglas 5 months ago - 2 comments

#44 - Error when using Pip to install phydms

Issue - State: closed - Opened by kevinmyers 6 months ago - 2 comments

#43 - Incompatibility with recent numpy version

Issue - State: open - Opened by gavinmdouglas 7 months ago

#42 - Can phydms calculate dN/dS ratios for entire genes in phylogeny?

Issue - State: closed - Opened by cahuparo almost 2 years ago - 1 comment

#41 - unpin `biopython`

Pull Request - State: closed - Opened by jbloom over 3 years ago

#40 - no `usetex` for matplotlib fonts in logo plots

Pull Request - State: closed - Opened by jbloom almost 4 years ago - 1 comment

#39 - phydms_plotselection

Issue - State: closed - Opened by Hamil462 about 4 years ago - 3 comments

#38 - Lint the code

Pull Request - State: closed - Opened by skhilton about 4 years ago

#37 - Scipy deprecation warnings

Pull Request - State: closed - Opened by skhilton about 4 years ago

#36 - Rel fdr

Pull Request - State: open - Opened by jon-mah over 4 years ago - 1 comment

#35 - ;sRel fdr

Pull Request - State: closed - Opened by jon-mah over 4 years ago

#34 - Rel FDR

Pull Request - State: closed - Opened by jon-mah over 4 years ago

#33 - Rel fdr

Pull Request - State: closed - Opened by jon-mah over 4 years ago

#32 - Rel names

Pull Request - State: closed - Opened by skhilton over 4 years ago

#31 - tweaks to documentation

Pull Request - State: closed - Opened by skhilton over 4 years ago

#30 - Implement Random-Effects-Likelihood Method

Pull Request - State: open - Opened by jon-mah over 4 years ago - 4 comments

#28 - shortened headers to 253 characters downstream of mafft

Pull Request - State: closed - Opened by skhilton over 4 years ago - 1 comment

#27 - fix `scipy` 2.0.0 deprecation warnings (ver 2.3.7)

Pull Request - State: closed - Opened by jbloom over 4 years ago - 1 comment

#26 - FloatingPointError: divide by zero encountered in true_divide

Issue - State: open - Opened by SternLabTAU over 4 years ago - 11 comments

#25 - `phydms_prepalignment` protein dictionary key error

Issue - State: closed - Opened by skhilton over 4 years ago - 3 comments
Labels: bug

#24 - replace bound on max stringency

Pull Request - State: closed - Opened by jbloom almost 5 years ago - 3 comments

#23 - Increased max bound for stringency parameter

Pull Request - State: closed - Opened by jbloom almost 5 years ago - 1 comment

#22 - `phydms_comprehensive` output CSV model comparison

Pull Request - State: closed - Opened by jbloom almost 5 years ago - 3 comments

#21 - start testing on python 3.6 and 3.7

Pull Request - State: closed - Opened by jbloom almost 5 years ago - 2 comments

#20 - removed reference to deprecated function select

Pull Request - State: closed - Opened by skhilton about 5 years ago - 2 comments

#19 - Pandas deprecation fix

Pull Request - State: closed - Opened by skhilton about 5 years ago

#18 - incompatibile with `pandas` 0.25

Issue - State: closed - Opened by jbloom about 5 years ago - 1 comment

#17 - option for single color in logo plots

Pull Request - State: closed - Opened by jbloom over 5 years ago

#16 - DMS2_batch_prefs MCMC does not converge on certain ENV sites

Issue - State: closed - Opened by jiroop almost 6 years ago - 1 comment

#15 - Q values should be for one sided tests?

Issue - State: closed - Opened by jbloom about 7 years ago - 1 comment

#14 - `scipy` convergence but Jacobian still large

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

#13 - examples of `YNGKP_M0` *not* optimizing

Issue - State: closed - Opened by skhilton over 7 years ago - 5 comments

#12 - `--diffprefsbysite` does **not** work with `--gammaomega`

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

#11 - underflow error with HIV and `--brlen optimize`

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

#10 - `phydms_logoplot` does not create new output directory

Issue - State: closed - Opened by skhilton over 7 years ago

#9 - `phydms_testdivpressure` broken

Issue - State: closed - Opened by jbloom over 7 years ago

#8 - `--brlen` does not accept "fix" as an argument

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

#7 - Underflow error with `YNGKP_M5`

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

#6 - check `divPressureValues` in `ExpCM_empirical_phi_divpressure`

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

#5 - some tweaks to phydms_testdivpressure

Issue - State: closed - Opened by jbloom about 8 years ago

#4 - list index out of range in phydms_prepalignments

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

#3 - Sites in ExpCM preferences file must start with 1?

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

#1 - Option to specify one ExpCM to use for averaged and randomized control models

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