Micha Sam Brickman Raredon comments

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                                            Micha Sam Brickman Raredon

Error in plot_cells - None of the provided genes were found in the cds

In my case, this turned out to be an error propagated from using SeuratWrappers to convert from a Seurat object to a Monocle object. The stepwise conversion discussed in this...

Running ALRA with multiple samples

I also have come to the conclusion that merging and then imputing with ALRA seems to work "better", in that the imputed data done this way seems to preserve more...

Running NICHES on large spatial datasets

1. Bug #37 part A above is a data-handling bug internal to NICHES, and can be by-passed, for now, by limiting the input object to just genes in your ground...

Running NICHES on large spatial datasets

Bug #37 part B above is a edge-list efficiency/scaling bug that is fixed by AOZ in the 'msbr_explorations' branch currently

Running NICHES on large spatial datasets

Release v.1.2.0 fixes this issue

Do we have scanpy version of NICHS

1. NICHES can handle matrix input and also be set to output matrices, this allows cross-compatibility with python environments. Currently, NICHES requires seurat to run, though we are working on...

Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double)

this is fixed in release v1.2.0

Extending spatial NICHES to 3D

If you have demo data that we could try to engineer this on, we would be very interested and willing to try. Would need to see the data structure to...