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INCATools
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biosample-analysis
analysis of biosamples in INSDC
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API methods to generate additional summary rows for Biosample table
#82
realmarcin
opened
2 years ago
0
provide NER output from SQLlite/basex tables
#81
realmarcin
opened
2 years ago
0
generate parquet file from SQLite/basex data
#80
realmarcin
opened
2 years ago
0
add Bioproject ids to Biosample records
#79
realmarcin
opened
2 years ago
0
decide on release artifacts
#78
wdduncan
opened
3 years ago
3
diff without running basex
#77
turbomam
closed
3 years ago
1
Minimal accounting of SQLite vs XQuery columns
#76
turbomam
closed
7 months ago
0
#74 wiped recipes that should stay in issue 61
#75
turbomam
closed
3 years ago
1
revert Makefile recipes that weren't ready for master
#74
turbomam
closed
7 months ago
0
cleanup commit 441a5fab9fca307e09bdd351176736a85b6cc3b2
#73
turbomam
closed
7 months ago
0
Issue #61 xquery
#72
turbomam
closed
3 years ago
0
reorganize notebooks directory
#71
turbomam
closed
7 months ago
0
Reconsider pasting of entrez link parts
#70
turbomam
closed
7 months ago
0
Have been inconsistent about joining and splitting on "|" vs "|||"
#69
turbomam
closed
7 months ago
0
Include local ontology's labels in human review spreadsheet
#68
turbomam
closed
7 months ago
1
scoped_mapping_of_biosamples_mixs check existing SSSOMs before OLS
#67
turbomam
closed
7 months ago
0
Can't find issue for reconciling curated NMDC ENVO subsets with INSDC ustilized terms
#66
turbomam
opened
3 years ago
2
Find some patterns of dubious mappings to discuss with SMEs
#65
turbomam
closed
7 months ago
5
use consistent case for ontology names
#64
turbomam
opened
3 years ago
0
repairing env_sample and mixs triad within biosample-analysis
#63
turbomam
opened
3 years ago
0
scoped_mapping_of_biosamples_mixs "value is trying to be set on a copy of a slice"
#62
turbomam
closed
7 months ago
0
rebuild harmonized_table with xquery & Bill's Perl pivot
#61
turbomam
closed
7 months ago
1
Where did these folders come from?
#60
turbomam
closed
7 months ago
1
.gitignore additions in master
#59
turbomam
opened
3 years ago
2
make harmonized_table.db: no sars_cov_2_diag_pcr_ct_value_2 column
#58
turbomam
closed
7 months ago
5
Perl modules required by Makefile recipes
#57
turbomam
closed
7 months ago
1
can't make target/emp_studies.tsv: empty CSV key at downloads/emp_studies.csv line 1
#56
turbomam
closed
7 months ago
3
target/%MIxS_columns.tsv target contains no %
#55
turbomam
closed
7 months ago
0
notebook showing MIxS comparison per #53
#54
hrshdhgd
closed
3 years ago
2
Map biosample table fields to MIxS packages
#53
realmarcin
closed
3 years ago
6
expected fields errors when reading full biosample tsv with pandas
#52
realmarcin
opened
3 years ago
1
add additional biosample identifiers as columns
#51
realmarcin
opened
3 years ago
1
Ontobio angle
#50
hrshdhgd
opened
3 years ago
1
target/occurrences-%.tsv make recipe can't find tabs
#49
turbomam
closed
7 months ago
2
Issue 47: create one-hot encode file of nmdc gold biosample data using runNER output
#48
wdduncan
closed
2 years ago
0
create one-hot encodings of nmdc biosample runNER output
#47
wdduncan
closed
2 years ago
0
Issue 44: create NMDC biosample file for OGER/runNER
#46
wdduncan
closed
3 years ago
1
issue-44: add NMDC biosample table with columns needed for NER to downloads
#45
wdduncan
closed
3 years ago
0
create NMDC biosample file for OGER/runNER
#44
wdduncan
closed
3 years ago
4
issue-40: get counts of distinct mixs triads
#43
wdduncan
closed
3 years ago
1
add make command to sync biosample files
#42
wdduncan
closed
7 months ago
0
starting to get envo friendly cols
#41
turbomam
closed
7 months ago
0
get counts of distinct mixs triads
#40
wdduncan
closed
3 years ago
1
add target that executes notebook from make
#39
wdduncan
closed
3 years ago
0
Build classifier using biosample training data
#38
realmarcin
opened
3 years ago
0
extract doi attibutes
#37
wdduncan
closed
3 years ago
0
add DOI to pivot table
#36
wdduncan
closed
3 years ago
0
experimental factor
#35
cmungall
opened
3 years ago
0
Xml parsing hhegde
#34
hrshdhgd
closed
3 years ago
1
Pushing notebook and output file. addresses #1
#33
hrshdhgd
closed
3 years ago
0
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