issues
search
jbloomlab
/
phydms
phylogenetic analyses informed by deep mutational scanning data
GNU General Public License v3.0
14
stars
4
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Error when using Pip to install phydms
#47
mokiine
closed
3 weeks ago
2
Tutorial typo fix
#46
gavinmdouglas
closed
4 months ago
0
Typo in tutorial?
#45
gavinmdouglas
closed
4 months ago
2
Error when using Pip to install phydms
#44
kevinmyers
closed
6 months ago
2
Incompatibility with recent numpy version
#43
gavinmdouglas
opened
7 months ago
0
Can phydms calculate dN/dS ratios for entire genes in phylogeny?
#42
cahuparo
closed
2 years ago
1
unpin `biopython`
#41
jbloom
closed
3 years ago
0
no `usetex` for matplotlib fonts in logo plots
#40
jbloom
closed
3 years ago
1
phydms_plotselection
#39
Hamil462
closed
4 years ago
3
Lint the code
#38
skhilton
closed
4 years ago
0
Scipy deprecation warnings
#37
skhilton
closed
4 years ago
0
Rel fdr
#36
jon-mah
opened
4 years ago
1
;sRel fdr
#35
jon-mah
closed
4 years ago
0
Rel FDR
#34
jon-mah
closed
4 years ago
0
Rel fdr
#33
jon-mah
closed
4 years ago
0
Rel names
#32
skhilton
closed
4 years ago
0
tweaks to documentation
#31
skhilton
closed
4 years ago
0
Implement Random-Effects-Likelihood Method
#30
jon-mah
opened
4 years ago
4
change `scipy.XXX` to `numpy.XXX` for `scipy 2.0.0` deprecation warning
#29
skhilton
closed
4 years ago
0
shortened headers to 253 characters downstream of mafft
#28
skhilton
closed
4 years ago
1
fix `scipy` 2.0.0 deprecation warnings (ver 2.3.7)
#27
jbloom
closed
4 years ago
1
FloatingPointError: divide by zero encountered in true_divide
#26
SternLabTAU
opened
4 years ago
11
`phydms_prepalignment` protein dictionary key error
#25
skhilton
closed
4 years ago
3
replace bound on max stringency
#24
jbloom
closed
4 years ago
3
Increased max bound for stringency parameter
#23
jbloom
closed
4 years ago
1
`phydms_comprehensive` output CSV model comparison
#22
jbloom
closed
4 years ago
3
start testing on python 3.6 and 3.7
#21
jbloom
closed
4 years ago
2
removed reference to deprecated function select
#20
skhilton
closed
5 years ago
2
Pandas deprecation fix
#19
skhilton
closed
5 years ago
0
incompatibile with `pandas` 0.25
#18
jbloom
closed
4 years ago
1
option for single color in logo plots
#17
jbloom
closed
5 years ago
0
DMS2_batch_prefs MCMC does not converge on certain ENV sites
#16
jiroop
closed
5 years ago
1
Q values should be for one sided tests?
#15
jbloom
closed
6 years ago
1
`scipy` convergence but Jacobian still large
#14
skhilton
closed
7 years ago
3
examples of `YNGKP_M0` *not* optimizing
#13
skhilton
closed
7 years ago
5
`--diffprefsbysite` does **not** work with `--gammaomega`
#12
jbloom
closed
4 years ago
1
underflow error with HIV and `--brlen optimize`
#11
skhilton
closed
7 years ago
3
`phydms_logoplot` does not create new output directory
#10
skhilton
closed
7 years ago
0
`phydms_testdivpressure` broken
#9
jbloom
closed
7 years ago
0
`--brlen` does not accept "fix" as an argument
#8
skhilton
closed
7 years ago
1
Underflow error with `YNGKP_M5`
#7
skhilton
closed
7 years ago
3
check `divPressureValues` in `ExpCM_empirical_phi_divpressure`
#6
jbloom
closed
7 years ago
1
some tweaks to phydms_testdivpressure
#5
jbloom
closed
8 years ago
0
list index out of range in phydms_prepalignments
#4
mbdoud
closed
8 years ago
1
Sites in ExpCM preferences file must start with 1?
#3
mbdoud
closed
8 years ago
1
hacked solution to nan problem with useLog and negative infinity problem without useLog
#2
jbloom
closed
8 years ago
1
Option to specify one ExpCM to use for averaged and randomized control models
#1
mbdoud
closed
8 years ago
1