psathyrella partis issues

psathyrella / partis

B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction

GNU General Public License v3.0

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issues

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Singularity

#328 ashotmarg closed 3 months ago
1
Issue with annotate

#327 ayeletperes closed 3 months ago
5
Issues with COAR

#326 psathyrella opened 4 months ago
1
Table of contents entries for command line scripts in auto generated sphinx docs are confusing

#325 psathyrella closed 7 months ago
1
get-tree-metrics action error

#324 bio-liucheng closed 8 months ago
4
Python version in docker: circle-plots.py

#323 ashotmarg opened 8 months ago
25
Docker container scipy versioning

#322 samkleeman1 closed 4 months ago
4
KeyError when using --extra-annotation-columns

#321 m-vieira closed 1 year ago
2
Dockerfile

#320 ashotmarg opened 1 year ago
10
Updated macaque IMGT alignments

#319 scharch closed 2 years ago
1
Mismatch between default and IMGT-aligned databases for macaques

#318 scharch closed 2 years ago
0
AIRR output crashes trying to call get_droplet_id

#317 ressy closed 2 years ago
5
A few fixes to the docs

#316 ressy closed 2 years ago
2
Fully switch to quay.io

#315 psathyrella closed 1 year ago
0
Add github actions

#314 jgallowa07 closed 1 year ago
1
simulating paired chains

#313 andreirajkovic closed 2 years ago
13
disable germline inference

#312 krishnaroskin closed 4 months ago
7
AIRR output with paired-loci

#311 elijgarcia closed 3 years ago
17
Partis Killed - no other error message

#310 lindsly closed 3 years ago
10
Assertion error when annotating

#309 NikaAb closed 3 years ago
9
Fix super-long insertions/deletions in large, high-mutation families

#308 psathyrella closed 3 years ago
3
Error in bcrham forward: sequences different length in Glomerator::NaiveHfrac

#307 nannabarnkob closed 3 years ago
10
recommendation for non-stranded reads?

#306 alexpan82 closed 3 years ago
3
Simulating with user-defined parameters

#305 aeonsofmusic closed 3 years ago
2
Converting partis partition yaml to AIRR tsv

#304 alexpan82 closed 4 years ago
7
Error using simulate function

#303 aeonsofmusic closed 4 years ago
2
Crash running partis partition

#302 m-vieira closed 4 years ago
4
Crash when running plot-partitions on output of partis partition run.

#301 wfs-lilly closed 4 years ago
1
Crash when using get-tree-metrics on output of partis partition run.

#300 wfs-lilly closed 4 years ago
5
partis partition crash

#299 wfs-lilly closed 4 years ago
1
Chicken sequence annotation

#298 nannabarnkob closed 4 years ago
10
get tree metrics for all partitions

#297 sravani9408 closed 4 years ago
2
utils.get_linearham_bounds comments, debug statements, small changes

#296 eharkins closed 4 years ago
0
process linearham annotations

#295 eharkins closed 4 years ago
0
linearham-info additions

#294 eharkins closed 4 years ago
0
Add indelutils.restrict_to_compatible_indels

#293 eharkins closed 5 years ago
0
treating VJ bounds shifting as a kwarg

#292 dunleavy005 closed 5 years ago
0
fixing igk/igl flexbounds/relpos handling

#291 dunleavy005 closed 5 years ago
0
flexbounds/relpos for igk/igl data

#290 dunleavy005 closed 5 years ago
0
flexbounds/relpox expanded for igk/igl data

#289 dunleavy005 closed 5 years ago
0
Add option to simulate with inferred clonal family size distribution

#288 psathyrella closed 3 years ago
1
Naming of novel alleles with large numbers of SNPs?

#287 scharch closed 5 years ago
2
Exceeded max number of tries for cmd

#286 NikaAb closed 5 years ago
2
Choosing positions to test for allele finding

#285 scharch closed 5 years ago
8
No partition in the output

#284 NikaAb closed 5 years ago
2
--presto-output not working if novel alleles are inferred

#283 williamdlees closed 5 years ago
9
Error with Partis when running Sumrep

#282 Pezhvuk closed 5 years ago
3
germline inference from bad sequences

#281 scharch closed 5 years ago
5
partition -> cluster label change

#280 dunleavy005 closed 5 years ago
0
Sequences marked as unproductive for unknown reasons

#279 nannabarnkob closed 5 years ago
6