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NBISweden
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IgDiscover-legacy
Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads
https://www.igdiscover.se
MIT License
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Clean up configuration
#74
marcelm
closed
10 months ago
0
Make computation of Ds_exact configurable
#73
marcelm
closed
7 years ago
0
The filtering step uses too much memory
#72
marcelm
closed
7 years ago
1
Merge parse and igblast scripts
#71
marcelm
closed
7 years ago
1
Make final iteration optional
#70
marcelm
closed
6 years ago
3
Add a column with number of barcodes to candidates list
#69
marcelm
closed
7 years ago
0
Make it possible to not collapse by barcode
#68
marcelm
closed
7 years ago
0
germlinefilter: Add a Ds_exact column
#67
marcelm
closed
7 years ago
0
plotalleles: Allow plotting D vs J
#66
marcelm
closed
10 months ago
0
Create a list of seen Ds as part of the normal pipeline
#65
marcelm
closed
7 years ago
2
Always run discoverj as part of the pipeline
#64
marcelm
closed
7 years ago
0
Add allele-ratio filtering to discoverj
#63
marcelm
closed
7 years ago
0
Add an allele ratio filter
#62
marcelm
closed
7 years ago
0
Set default no. of iterations to 1
#61
marcelm
closed
7 years ago
0
Create identity-divergence plots
#60
marcelm
closed
10 months ago
0
Add a D_errors column to the assigned.tab file
#59
marcelm
closed
7 years ago
1
Get inspiration from giggle
#58
marcelm
closed
10 months ago
0
germlinefilter: Discard cross-mapping artifacts even if they are whitelisted
#57
marcelm
closed
7 years ago
1
Cross-mapping correction is order-dependant
#56
marcelm
closed
7 years ago
1
Document new differences=0 default
#55
marcelm
closed
7 years ago
0
Make cross mapping ratio = 0.1 the default
#54
marcelm
closed
7 years ago
2
Ensure the meaning of "db" in candidates.tab is documented
#53
marcelm
closed
7 years ago
1
Make a new release soon
#52
marcelm
closed
7 years ago
1
Set up test environment with miniconda
#51
marcelm
closed
7 years ago
0
Possibly use 'exact' column to compute cross-mapping ratio
#50
marcelm
closed
10 months ago
0
make differences = 0 the default
#49
marcelm
closed
7 years ago
0
Reported cluster_size for artificially added "db" sequences may be wrong
#48
marcelm
closed
7 years ago
2
Couple changes
#47
marcelm
closed
7 years ago
1
Be more helpful when validating the input database
#46
marcelm
closed
7 years ago
2
Set up testing with Travis
#45
marcelm
closed
7 years ago
1
Link to image
#44
jhagberg
closed
7 years ago
1
Tests for more subcommands
#43
marcelm
closed
10 months ago
0
Assign clonotype to a small number of sequences
#42
marcelm
closed
7 years ago
1
Count and report clonotypes
#41
marcelm
closed
7 years ago
3
Spawn only as many igblastn processes as cores
#40
marcelm
closed
7 years ago
2
Print IgBLAST speed and/or progress
#39
marcelm
closed
7 years ago
0
Remove warning: "wildcard constraints in inputs are ignored"
#38
marcelm
closed
7 years ago
2
Make a demo result available for download
#37
marcelm
closed
10 months ago
0
Update test data set to reflect new file names
#36
marcelm
closed
7 years ago
1
Make rename: false the default?
#35
marcelm
closed
7 years ago
1
Draw a graph of similar novel sequences
#34
marcelm
closed
10 months ago
0
Omit species from database file names
#33
marcelm
closed
7 years ago
1
Discover J genes
#32
marcelm
closed
7 years ago
1
Require sequence structure at 3' end: primer + barcode
#31
marcelm
closed
10 months ago
1
For cross-mapping correction, ignore last 5 bases
#30
marcelm
closed
7 years ago
1
Display mailing list address in documentation
#29
marcelm
closed
7 years ago
2
_pickle.PicklingError
#28
marcelm
closed
7 years ago
2
Do not rename sequences identical to a starting database sequence
#27
marcelm
closed
7 years ago
1
Require fewer sequences for errorplots
#26
marcelm
closed
7 years ago
1
Allow to relax pre-processing filter criteria
#25
marcelm
closed
7 years ago
3
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