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phac-nml
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staramr
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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Release Candidate Changes
#62
jennifertran
closed
5 years ago
2
Revert ResFinder/PointFinder default to previous release versions
#61
apetkau
closed
5 years ago
1
Fixed index range error and added integration test
#60
jennifertran
closed
5 years ago
1
Determine best approach to integrating typing information in staramr
#59
apetkau
closed
5 years ago
1
Added --ignore-invalid-files command and better error message for invalid inputs
#58
jennifertran
closed
5 years ago
1
Updated README.md to include PlasmidFinder
#57
jennifertran
closed
5 years ago
1
Add support for enterococcus faecium
#56
mjram0s
closed
5 years ago
2
Update documentation for staramr to include plasmidfinder
#55
apetkau
closed
5 years ago
1
Compare results between plasmidfinder/staramr and existing plasmidfinder web application
#54
apetkau
closed
5 years ago
1
Added option to select which type of plasmidfinder database
#53
jennifertran
closed
5 years ago
1
Add support for multiple types of biological data files
#52
apetkau
opened
5 years ago
1
Add an option to select between the enterobacteriacae and gram_positive files
#51
jennifertran
closed
5 years ago
1
Added Detailed Summary Report
#50
jennifertran
closed
5 years ago
3
Added Plasmid Genes to summary table
#49
jennifertran
closed
5 years ago
2
Make %id and %length adjustable and set defaults (80% id over 60% length)
#48
apetkau
closed
5 years ago
1
Construct new report incorporating resistance genes and plasmids
#47
apetkau
closed
5 years ago
2
Incorporation of plasmids in final report
#46
apetkau
closed
5 years ago
1
Added python green test runner to travis
#45
jennifertran
closed
5 years ago
1
Results not matching CGE ResFinder web-interface output
#44
eam12
closed
5 years ago
2
Add plasmidfinder and tests
#43
jennifertran
closed
5 years ago
1
Release candidate 0.4.0
#42
apetkau
closed
5 years ago
0
Fix python 3.5
#41
apetkau
closed
5 years ago
0
Added cmd line options for PlasmaFinder
#40
jennifertran
closed
5 years ago
2
Add command line options for Plasmid Finder
#39
jennifertran
closed
5 years ago
1
Detection of plasmid genes using plasmidfinder database
#38
apetkau
closed
5 years ago
0
Added plasmid db and unit tests
#37
jennifertran
closed
5 years ago
2
Update databases
#36
apetkau
closed
5 years ago
0
Add enterococcus faecalis support
#35
mjram0s
closed
5 years ago
1
Remove deprecated read_table calls and replace with read_csv
#34
mjram0s
closed
5 years ago
1
Update pandas read_table to read_csv
#33
mjram0s
closed
5 years ago
0
Add campylobacter support
#32
mjram0s
closed
5 years ago
1
Refactor and mypy typechecking
#31
apetkau
closed
5 years ago
0
Add ability to load and update plasmid databases
#30
apetkau
closed
5 years ago
1
Background reading on plasmid databases/detection
#29
apetkau
closed
5 years ago
0
Fix/exclude genes
#28
apetkau
closed
5 years ago
0
aac(6')-Iaa is falsley mapped to gentamicin resistance when it should not be
#27
apetkau
closed
5 years ago
1
Specify which versions of BLAST staramr will work with
#26
apetkau
closed
2 years ago
1
Add better error message/handling in case of empty input file
#25
apetkau
closed
5 years ago
1
Fix up issue when sequence id was a number
#24
apetkau
closed
5 years ago
2
Unexpected crashes on some FASTA files
#23
kbessonov1984
closed
5 years ago
2
Update database
#22
apetkau
closed
5 years ago
1
Add check for duplicate sequence IDs in input files
#21
apetkau
closed
5 years ago
2
Error message returned non-zero exit status 1
#20
SK-N-BE
closed
6 years ago
5
Fix handling of spaces in Galaxy tool
#19
apetkau
closed
6 years ago
1
staramr in Galaxy error
#18
PHemarajata
closed
6 years ago
4
Add support for additional PointFinder organisms
#17
apetkau
closed
1 year ago
1
Feature/update drugtable other fixes
#16
apetkau
closed
6 years ago
4
Database restore and invert BLAST
#15
apetkau
closed
6 years ago
0
Feature/blast tabular
#14
apetkau
closed
6 years ago
0
pointfinder db results DataFrame is None; AttributeError: 'NoneType' object has no attribute 'to_csv'
#13
peterk87
closed
6 years ago
3
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