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pepkit
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geofetch
Builds a PEP from SRA or GEO accessions
https://pep.databio.org/geofetch/
BSD 2-Clause "Simplified" License
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Add example to the cli
#89
khoroshevskyi
closed
1 year ago
0
geofetch after refactoring doesn't download SRA data
#88
khoroshevskyi
closed
1 year ago
0
Refactoring + improvements in retrieving peppy project + fixed few bugs
#87
khoroshevskyi
closed
1 year ago
3
Add more tests
#86
khoroshevskyi
closed
1 year ago
0
Delete old geofetch website
#85
khoroshevskyi
closed
2 years ago
1
peppy init and progress bar
#84
khoroshevskyi
closed
2 years ago
1
raw projects don't have subfolders
#83
khoroshevskyi
closed
1 year ago
0
Issues in getting sra file with post request
#82
khoroshevskyi
closed
1 year ago
4
Create peppy object by using geofetch
#81
khoroshevskyi
closed
1 year ago
0
`yaml.scanner.ScannerError` when initializing PEP downloaded with `geofetch`
#80
nleroy917
closed
1 year ago
1
Switch From `subprocess` and `wget` to `requests` module
#79
nleroy917
closed
1 year ago
0
V0.10.1
#78
khoroshevskyi
closed
2 years ago
1
The usage of the eutils must be improved
#77
khoroshevskyi
closed
2 years ago
0
version 0.10.0
#76
khoroshevskyi
closed
2 years ago
2
Dev alex
#75
khoroshevskyi
closed
2 years ago
1
Fail to download GSExxxxxx_SRA.csv
#74
shkao
closed
2 years ago
2
Add progress bar
#73
khoroshevskyi
closed
1 year ago
2
Gracefully Terminate Child Subprocesses
#72
nleroy917
closed
2 years ago
4
Sanitize sample names
#71
nleroy917
closed
2 years ago
3
Ability create `.pep.yaml` files
#70
nleroy917
closed
2 years ago
1
version 0.9.0
#69
khoroshevskyi
closed
2 years ago
23
make columns case insensitive
#68
khoroshevskyi
closed
2 years ago
2
Error while using --filter-size
#67
khoroshevskyi
closed
2 years ago
0
Disable creating huge combined pep
#66
nsheff
closed
2 years ago
0
Large, constant sample attributes should be moved to project config
#65
nsheff
closed
2 years ago
2
Incorrect help --data-source description
#64
khoroshevskyi
closed
2 years ago
0
Docs build failing
#63
nsheff
closed
2 years ago
1
Error giving sample list file
#62
nsheff
closed
2 years ago
1
Release version 0.8.0
#61
nsheff
closed
2 years ago
2
The argument --acc-anno is not working for processed data
#60
khoroshevskyi
closed
2 years ago
0
input sample lists are not working for processed data
#59
khoroshevskyi
closed
2 years ago
1
input sample lists are not working
#58
nsheff
closed
2 years ago
0
In series annotation file files are stored in the list
#57
khoroshevskyi
closed
2 years ago
0
Decouple Geofetcher and argparser
#56
khoroshevskyi
closed
2 years ago
3
Clean up soft files
#55
khoroshevskyi
closed
2 years ago
1
Don't use absolute hard paths in output PEPs
#54
nsheff
closed
2 years ago
0
Mkdocs build failing
#53
nsheff
closed
2 years ago
4
Unit tests
#52
nsheff
closed
2 years ago
2
Incorrect path in PEP to the downloaded files
#51
khoroshevskyi
closed
2 years ago
1
Code blocking
#50
nsheff
closed
2 years ago
4
bring in latest master changes
#49
nsheff
closed
2 years ago
0
Fix PyPI readme formatting
#48
nsheff
closed
2 years ago
6
Metadata standardization
#47
khoroshevskyi
opened
2 years ago
3
Integration of geofetch and pephub
#46
khoroshevskyi
closed
1 year ago
3
Adding filter that separates experiment and sample data
#45
khoroshevskyi
closed
2 years ago
2
Add file size filter for processed files
#44
khoroshevskyi
closed
2 years ago
8
Geofetch code blocking and improvements
#43
khoroshevskyi
closed
2 years ago
0
ignore case in filter regex
#42
stolarczyk
closed
2 years ago
1
NameError: name 'Sys' is not defined
#41
stolarczyk
closed
2 years ago
1
update to new pipeline interface
#40
nsheff
closed
2 years ago
0
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