matsengrp / linearham

A Bayesian Phylo-HMM for B cell receptor sequence analysis

http://matsengrp.github.io/linearham

matsengrp/linearham Issues

figure out why output dir has to be under `/linearham`
Updated 2 years ago7
Failed Quay build from trigger
Closed 2 years ago
update readme with newer (?) output files
Closed 2 years ago2
How to handle paired h/l data
Closed 2 years ago
Add option for less verbose output dir
Closed 2 years ago1
Github Actions & Quay Container building
Closed 2 years ago2
Use new partis fcn add_seqs_to_line()
Closed 2 years ago4
Cause of huge number of low-probability nodes
Closed 2 years ago6
Branch lengths almost all much larger than hamming distance
Updated 2 years ago
Inferred ancestral sequences have mutations in ambiguous regions
Updated 2 years ago
crash in asr/ess script
Closed 2 years ago7
Update Master -> Main
Closed 3 years ago
Docker container doesn't build
Closed 3 years ago2
light chain crash
Updated 3 years ago3
update partis + maybe add --min-cluster-size arg
Closed 3 years ago1
make default tag on quay.io
Closed 4 years ago1
change actions to positional argument
Closed 4 years ago
NodeList object where it expected a string
Closed 4 years ago1
linearham crashed
Closed 4 years ago7
SCons not recognizing arguments to linearham?
Closed 4 years ago3
git describe crashes build
Closed 4 years ago1
remove mention of ubuntu 16.04 from readme
Closed 4 years ago4
Do we really want to use scons?
Closed 4 years ago3
remove dockerhub image
Closed 4 years ago1
Docker runs example and quits
Closed 4 years ago5
linearham processing failure -- need help interpreting/solving error message
Closed 5 years ago4
Can't seem to get linearham to run -- probably an issue understanding inputs
Closed 5 years ago6
Add more info to manual
Closed 5 years ago1
Docker image missing mafft
Closed 5 years ago33
Add c++ exception when reading null flexbounds
Closed 5 years ago
biological validation data sets
Closed 5 years ago1
linearham 2.0: the Awakening
Closed 6 years ago4
Add a simple CLI
Closed 6 years ago
Python wrapper which builds an initial tree
Closed 6 years ago2
Remove matrix copy construction in Smooshable et al constructors?
Closed 6 years ago4
Viterbi calculations in the NTI region are incorrect
Closed 6 years ago12
We should be using the Eigen Index type for indexing
Closed 6 years ago1
Disable copy constructors?
Closed 6 years ago1
Split test cases into sections?
Closed 6 years ago1
B-W or stochastic EM?
Closed 6 years ago2
What do we do with N bases in the middle of a read?
Closed 6 years ago1
Compare to bcrham
Closed 8 years ago15
Give germline-encoded Smooshables pointers back to their Germline objects
Closed 6 years ago1
Designing a Phylo object
Closed 6 years ago19
fix likelihood calculation
Closed 6 years ago2
Test creation of [VDJ]Smooshables
Closed 8 years ago1
Build object to contain all of the HMM information
Closed 8 years ago2
build an object to contain information from the partis CSV
Closed 8 years ago
Get partis SW results into linearham
Closed 8 years ago1
parse partis yaml and fit into Germline object
Closed 8 years ago1