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matsengrp
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cft
Clonal family tree
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Introduction on the program
#312
xuanmingshi
closed
2 years ago
1
Use new partis fcn add_seqs_to_line()
#311
psathyrella
opened
4 years ago
6
Validate parsing of partis multiplicity
#310
eharkins
closed
4 years ago
15
286 indel trees
#309
eharkins
closed
4 years ago
0
Nextflow
#308
eharkins
opened
4 years ago
0
update partis selection metrics
#307
eharkins
closed
4 years ago
0
Preserve ambiguous nucleotides
#306
eharkins
closed
4 years ago
1
Update partis selection metrics
#305
eharkins
closed
4 years ago
0
update partis get-selection-metrics/get-tree-metrics call
#304
psathyrella
closed
4 years ago
1
environment.yml
#303
eharkins
closed
4 years ago
0
170 raxml-ng
#302
eharkins
closed
4 years ago
0
299 cleanup
#301
eharkins
closed
4 years ago
0
partis utils.restrict_to_iseqs change
#300
eharkins
closed
4 years ago
0
Remove commented out / unused code and run code formatter
#299
eharkins
closed
4 years ago
0
update testing framework
#298
eharkins
opened
4 years ago
1
295 downsampling large clusters
#297
eharkins
closed
4 years ago
0
186 blast for observed ancestors
#296
eharkins
closed
4 years ago
0
Reconsider subsampling/pruning procedure
#295
eharkins
closed
4 years ago
19
Flow chart defining correspondence between Overbaugh and Matsen teams on B-cell research
#294
eharkins
closed
4 years ago
11
Output full partis cluster fasta
#293
eharkins
closed
4 years ago
2
274 alignment
#292
eharkins
closed
5 years ago
2
276 linearham integration
#291
eharkins
closed
5 years ago
0
Check whether naive was sampled
#290
eharkins
closed
4 years ago
1
273 process all part steps
#289
eharkins
closed
5 years ago
1
Track build options alongside input data
#288
eharkins
opened
5 years ago
1
Archiving data for manuscripts
#287
lauradoepker
closed
4 years ago
6
Add indel tree analysis to pipeline?
#286
eharkins
closed
4 years ago
9
Resolve insertion in QA255.016-VL
#285
eharkins
closed
5 years ago
2
281 process seed indels
#284
eharkins
closed
5 years ago
0
Olmsted frozen deployments
#283
matsen
closed
5 years ago
4
Make it very obvious when sequences have an indel
#282
matsen
closed
5 years ago
7
Add process_partis.py option for a specific indel
#281
eharkins
closed
5 years ago
6
improve view-output output
#280
psathyrella
closed
5 years ago
1
Investigate shm indel in QA255.157-Vk
#279
psathyrella
closed
5 years ago
10
Can we use synthetic spike-ins?
#278
psathyrella
opened
5 years ago
0
Indel handling in QA255.157-Vk
#277
lauradoepker
closed
5 years ago
9
Bayesian analysis integration
#276
matsen
opened
5 years ago
11
clean up glfo treatment
#275
psathyrella
closed
5 years ago
0
Remove cft alignment step
#274
psathyrella
opened
5 years ago
15
Do not process partis non-"best" partitions by default
#273
eharkins
closed
5 years ago
17
Use partis tree metrics script without calling annotate
#272
eharkins
closed
5 years ago
0
263 n total reads
#271
eharkins
closed
5 years ago
1
266 partis alt naive analysis
#270
eharkins
closed
5 years ago
1
268 timepoint reqs
#269
eharkins
closed
5 years ago
1
Stricter requirements for timepoint data
#268
eharkins
closed
5 years ago
4
Rename things to match olmsted terminology
#267
metasoarous
opened
5 years ago
0
Create logo plot from partis alternative naives
#266
eharkins
closed
5 years ago
4
264 annotation index
#265
eharkins
closed
5 years ago
6
Fix unchecked index in merge_selection_metrics.py
#264
eharkins
closed
5 years ago
5
Add version of `n_seqs` summing over multiplicity data
#263
metasoarous
closed
5 years ago
18
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