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gbouras13
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phold
Phage Annotation using Protein Structures
MIT License
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anti-CRISPR proteins get assigned the phrog cluster "acr" instead of a number
#71
Fabian-Bastiaanssen
opened
1 week ago
1
using phold plot
#70
r4carson
opened
3 weeks ago
1
[Request] GFF Output
#69
MJNT1999
closed
4 weeks ago
2
fix long header issues #67
#68
gbouras13
closed
1 month ago
0
long ids > 54 characters in genbank input introduce space
#67
gbouras13
closed
1 month ago
0
phold memory usage
#66
shiraz-shah
opened
1 month ago
6
fix plot error if all genes hypothetical
#65
gbouras13
closed
1 month ago
0
Fix #57
#64
gbouras13
closed
2 months ago
0
fix bug with `phold compare` with `--structures` crashing if extra structures in structure_dir
#63
gbouras13
closed
2 months ago
0
V0.2.1
#62
gbouras13
closed
2 months ago
0
Fix issue with torch using all available threads
#61
gbouras13
closed
2 months ago
0
[BUG] Limit CPU usage for 3Di prediction
#60
valentynbez
closed
2 months ago
2
phold.features.predict_3Di:get_embeddings:441 - Using models in half-precision
#59
emmaosei
opened
2 months ago
3
Add gff output
#58
gbouras13
closed
2 months ago
1
`phold proteins-predict` will silently fail if .gbk given as input
#57
gbouras13
closed
2 months ago
0
phold run error
#56
ChaoXianSen
opened
2 months ago
1
Error running `phold run` in Colab Notebook
#55
Noonanav
closed
2 months ago
3
Inquiry on protein annotation
#54
songmj86
opened
2 months ago
10
add workflow
#53
gbouras13
closed
2 months ago
0
add logo to docs
#52
gbouras13
closed
2 months ago
0
v0.2.0
#51
gbouras13
closed
2 months ago
0
phold install gets killed. Manually downloading the ProstT5 database doesn't fix the issue
#50
LSHillary
closed
2 months ago
2
Phold crashes when the start position is 0
#49
konstytucja
closed
2 months ago
2
Add .cif support to Phold
#48
gbouras13
closed
2 months ago
0
ProstT5 issue: iteration over a 0-d array
#47
vdruelle
closed
2 months ago
2
set db dir under PHOLD_DBDIR environement variable control
#46
EricDeveaud
closed
2 months ago
2
Problem with using custom phold database
#45
rozwalak
opened
3 months ago
0
Running Phold offline
#44
aponsero
closed
2 months ago
3
models--Rostlab--ProstT5_fp16 error with Downloading
#43
CynthiaChibani
closed
2 months ago
3
ValueError during Processing Foldseek output
#42
acvill
closed
2 months ago
3
KeyError when analyzing pharokka output
#41
mesti90
closed
3 months ago
2
OSError on phold install
#40
jonbakerlab
closed
4 months ago
5
Foldseek Version checking -
#39
gbouras13
closed
2 months ago
1
Add Phynteny to colab notebook and readme
#38
gbouras13
closed
5 months ago
0
ValueError: Columns must be same length as key
#37
kayanac
closed
5 months ago
7
PermissionError in `phold plot`
#36
Ulthran
opened
5 months ago
6
add tests for embeddings
#35
gbouras13
closed
5 months ago
0
add functionality to save embeddings
#34
gbouras13
closed
5 months ago
0
Questions regarding the proper use of phold
#33
bhagavadgitadu22
opened
6 months ago
3
v0.1.4
#32
gbouras13
closed
6 months ago
0
KeyError: 'transl_table' when writing genbank output
#31
btemperton
closed
6 months ago
2
v0.1.3
#30
gbouras13
closed
6 months ago
0
add second colab notebook and docs
#29
gbouras13
closed
6 months ago
0
notebook
#28
gbouras13
closed
6 months ago
0
v0.1.2
#27
gbouras13
closed
7 months ago
0
Minor fixes to README
#26
Vini2
closed
7 months ago
1
add history
#25
gbouras13
closed
7 months ago
0
Fix pypi issues, change structure, bump to v0.1.1
#24
gbouras13
closed
7 months ago
0
minor docs changes
#23
gbouras13
closed
7 months ago
0
Add opacity for probabilistic annotation
#22
gbouras13
opened
7 months ago
0
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