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airr-formats
PLEASE SEE airr-standards FOR FURTHER DEVELOPMENT: https://github.com/airr-community/airr-standards
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Frontiers article describing file formats
#56
laserson
closed
6 years ago
0
resolve alignments branch
#55
schristley
closed
6 years ago
1
Remove "(transferred from germline)" from docs
#54
laserson
closed
6 years ago
0
Changeo integration
#53
schristley
closed
6 years ago
0
Contribution to Frontiers?
#52
laserson
closed
6 years ago
2
Genbank structured comments
#51
laserson
closed
6 years ago
4
Changeo integration
#50
schristley
closed
6 years ago
3
Consider renaming "rearrangements" to "chains"?
#49
laserson
closed
6 years ago
4
sample_id should be pointing to a NucleicAcidProcessing object
#48
laserson
closed
6 years ago
8
Alignments table should have a key into the rearrangements
#47
laserson
closed
6 years ago
2
Change "sequence_id" to "rearrangement_id"?
#46
laserson
closed
6 years ago
10
[vdjc]_call VS [vdjc]_allele
#45
bcorrie
closed
6 years ago
10
Merge airr-formats and airr-standards
#44
laserson
closed
6 years ago
7
Reorganized scripts
#43
laserson
closed
6 years ago
0
Clarify duplicate and consensus counts
#42
laserson
closed
6 years ago
1
Clarified junction vs CDR3 issue
#41
laserson
closed
6 years ago
1
Update docs to reflect metadata in separate yaml/json file
#40
laserson
closed
6 years ago
0
Initial Travis setup
#39
laserson
closed
6 years ago
0
Update README and `docs/`
#38
matsen
closed
6 years ago
2
Convert yaml spec to swagger compatible schema definition
#37
schristley
closed
6 years ago
3
Evaluate work for supporting airr-format output
#36
laserson
closed
6 years ago
1
Write an R package
#35
laserson
closed
6 years ago
1
Set up Travis for checking spec consistency
#34
laserson
closed
6 years ago
1
rearrangements reconciliation
#33
laserson
closed
6 years ago
13
Two sample_type in Minimal Standard YAML files...
#32
bcorrie
closed
6 years ago
2
Minimal Standard "Study" vs Formats "Project"
#31
bcorrie
closed
6 years ago
6
move metadata from header to separate file
#30
schristley
closed
6 years ago
2
change write function to use csv.DictWriter
#29
schristley
closed
6 years ago
1
Add CIGAR notes to common doc
#28
laserson
closed
7 years ago
1
CDR3 vs junction
#27
javh
closed
6 years ago
10
Annotating alignment positions in the CIGAR string.
#26
javh
closed
7 years ago
16
Move general specs on our TSV dialect to a central location
#25
laserson
closed
7 years ago
0
How do we encode `cdr3_aa` in cases of out-of-frame sequences?
#24
laserson
closed
6 years ago
6
Add explicit docs on numbering scheme
#23
laserson
closed
6 years ago
7
`constant` in rearragements spec should be treated as alignment-derived
#22
laserson
closed
7 years ago
1
object definitions for minimal standards
#21
schristley
closed
6 years ago
1
Draft alignment spec for hit table
#20
laserson
closed
7 years ago
0
Refactor/cleanup python module
#19
laserson
closed
7 years ago
4
Which license do we give this work?
#18
laserson
closed
7 years ago
1
provides/requires tool metadata
#17
schristley
closed
7 years ago
2
finalize names
#16
schristley
closed
7 years ago
0
spec for tools adding new columns
#15
schristley
closed
7 years ago
4
Document how to pull out "primary" alignments with awk
#14
laserson
closed
7 years ago
1
Multisequence annotations (e.g., joint calling with partis)
#13
laserson
closed
7 years ago
31
Ensure you can represent heavy/light pairing
#12
laserson
closed
7 years ago
0
How do we deal with multiple sequences that are jointly annotated/called
#11
laserson
closed
7 years ago
1
FWR/CDR annotations
#10
laserson
closed
7 years ago
11
Finalize field names
#9
laserson
closed
7 years ago
10
Finalize mandatory/non-mandatory
#8
laserson
closed
7 years ago
19
Add amino acid translations to schema
#7
laserson
closed
7 years ago
1
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