psathyrella / partis

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

psathyrella/partis Issues

Singularity
Closed 6 months ago1
Issue with annotate
Closed 7 months ago5
Issues with COAR
Updated 7 months ago1
Python version in docker: circle-plots.py
Updated 7 months ago25
Dockerfile
Updated 7 months ago10
disable germline inference
Closed 8 months ago7
Docker container scipy versioning
Closed 8 months ago4
get-tree-metrics action error
Closed a year ago4
Table of contents entries for command line scripts in auto generated sphinx docs are confusing
Closed a year ago1
KeyError when using --extra-annotation-columns
Closed 2 years ago2
Add github actions
Closed 2 years ago1
Fully switch to quay.io
Closed 2 years ago
AIRR output with paired-loci
Closed 3 years ago17
Mismatch between default and IMGT-aligned databases for macaques
Closed 2 years ago
AIRR output crashes trying to call get_droplet_id
Closed 3 years ago5
simulating paired chains
Closed 3 years ago13
Fix super-long insertions/deletions in large, high-mutation families
Closed 4 years ago3
Building bcrham failing with "undefined reference to YAML"
Closed 5 years ago12
Add option to simulate with inferred clonal family size distribution
Closed 4 years ago1
recommendation for non-stranded reads?
Closed 4 years ago3
Assertion error when annotating
Closed 4 years ago9
Partis Killed - no other error message
Closed 4 years ago10
Error in bcrham forward: sequences different length in Glomerator::NaiveHfrac
Closed 4 years ago10
Simulating with user-defined parameters
Closed 4 years ago2
Converting partis partition yaml to AIRR tsv
Closed 4 years ago7
Error using simulate function
Closed 5 years ago2
Chicken sequence annotation
Closed 5 years ago10
Crash when running plot-partitions on output of partis partition run.
Closed 5 years ago1
Crash running partis partition
Closed 5 years ago4
Crash when using get-tree-metrics on output of partis partition run.
Closed 5 years ago5
partis partition crash
Closed 5 years ago1
get tree metrics for all partitions
Closed 5 years ago2
Naming of novel alleles with large numbers of SNPs?
Closed 5 years ago2
Exceeded max number of tries for cmd
Closed 5 years ago2
--presto-output not working if novel alleles are inferred
Closed 5 years ago9
Error with Partis when running Sumrep
Closed 5 years ago3
Choosing positions to test for allele finding
Closed 5 years ago8
germline inference from bad sequences
Closed 5 years ago5
No partition in the output
Closed 5 years ago2
partis ignoring --extra-annotation-columns
Closed 6 years ago3
Suggested optimization/work-around for out of memory error?
Closed 6 years ago5
Sequences marked as unproductive for unknown reasons
Closed 6 years ago6
test
Closed 6 years ago
correct/update version information
Closed 6 years ago2
Confusing n procs status messages
Closed 6 years ago2
--n-alleles-per-gene parameter not working
Closed 6 years ago12
qr_gap_seq length not the same as qrbound length in v region indelfo
Closed 6 years ago3
template not in codon_info error?
Closed 6 years ago3
python2.7 must be given explicitly; cannot find `gsl`, `gsldev`
Closed 6 years ago7
Run error: yaml is needed, manually installed, keeps failing
Closed 6 years ago5