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Bayesian Gaussian Process Latent Variable Models for pseudotime inference in single-cell RNA-seq data
gpseudotime is the only instance of running GPLVM in Julia: bgplvm.jl.
Trying to run the gpseudotime.ipynb in the current version of Julia (0.5.2), I find that {} should be replaced by [] in bgplvm.jl.
The creation and update of data files in h5 gives me the following errors:
h5write(trace_file, "synthetic/X", X)
h5write(trace_file, "synthetic/n", n)
h5write(trace_file, "synthetic/lambda", lambda)
h5write(trace_file, "synthetic/sigma", sigma)
h5write(trace_file, "synthetic/t_gt", t_gt)
Error creating dataset //synthetic/X
in h5d_create(::Int32, ::String, ::Int32, ::Int32, ::Int32, ::Int32, ::Int32) at C:\Users\Denis.julia\v0.5\HDF5\src\HDF5.jl:2089
in d_create(::HDF5.HDF5File, ::String, ::HDF5.HDF5Datatype, ::HDF5.HDF5Dataspace, ::HDF5.HDF5Properties, ::HDF5.HDF5Properties, ::HDF5.HDF5Properties) at C:\Users\Denis.julia\v0.5\HDF5\src\HDF5.jl:809
in _d_create(::HDF5.HDF5File, ::String, ::Array{Float64,2}) at C:\Users\Denis.julia\v0.5\HDF5\src\HDF5.jl:1539
in _d_write(::HDF5.HDF5File, ::String, ::Array{Float64,2}) at C:\Users\Denis.julia\v0.5\HDF5\src\HDF5.jl:1560
in h5write(::String, ::String, ::Array{Float64,2}) at C:\Users\Denis.julia\v0.5\HDF5\src\HDF5.jl:613
Also synth_analysis.jl does not appear to be in the repository.
A re-run of this demo with updated packages would be appreciated.
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