kharchenkolab Baysor issues

kharchenkolab / Baysor

Bayesian Segmentation of Spatial Transcriptomics Data

MIT License

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issues

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clustering transcripts without segmentation

#127 araksm opened 1 week ago
0
create a squidpy or R object using baysor output

#126 shrutikhare-git opened 2 weeks ago
1
Output matrix formatted wrong for tsv

#125 Hannah-Doerpholz opened 2 weeks ago
0
Square root of negative value error during "using 3D coordinates"

#124 sapiomr opened 3 weeks ago
1
Installation of Baysor from Julia

#123 sdwien closed 1 month ago
1
Update merfish.toml

#122 sebherbert closed 2 weeks ago
1
The HTML file output by the baysor preview or baysor run command exceeds 1 GB, making it impossible to browse using a standard web browser.

#121 MOSAIFENG opened 1 month ago
0
Question about assignment of transcripts in overlapping regions

#120 Jwong684 opened 2 months ago
0
Loading binary image sementation mask as prior: MethodError: no method matching sparse

#119 Sengels24 opened 2 months ago
1
ERROR: LoadError: gene column 'target' not found in the data frame

#118 tsuijenk closed 2 months ago
0
--prior-segmentation-confidence=1 but contradict to prior_segmentation

#117 SanoKyohei opened 3 months ago
0
Error: Not enough prior cells pass the min_mols_per_cell=10 threshold

#116 quentinblampey opened 3 months ago
0
Version Flag states "nothing"

#115 JeffreyMaurer opened 3 months ago
0
Error while estimating local colours

#114 gargerd opened 3 months ago
1
Missing Transcript Plots with Preview

#113 matthewcormier95 opened 3 months ago
1
Error with downloading artifact of JpegTurbo; tree hash mismatch

#112 gretajuu opened 4 months ago
0
Running 3D Segmentation

#111 NickDiNapoli opened 5 months ago
3
Not producing loom file output

#110 dr-sayyadhury opened 5 months ago
0
Error in README

#109 Hannah-Doerpholz closed 5 months ago
1
add more channel

#108 andynkili opened 5 months ago
1
Baysor is killed unexpectedly

#106 sebherbert closed 6 months ago
1
Clarification on 'Warning: To many values of z. Using 2D polygons'

#105 e-manduchi opened 7 months ago
3
data file paths in docker and plotting

#104 pmaye opened 8 months ago
0
Baysor produces invalid polygons

#103 pakiessling opened 8 months ago
0
`boundary_polygons` not defined. Baysor v0.6.2

#102 tsvvas opened 9 months ago
3
Nuclear-expansion like approach

#101 maximilian-heeg opened 9 months ago
0
The output file "segmentation.csv" cell column value is NaN

#100 mzj0418 opened 9 months ago
0
Issues with running the STARmap example

#99 HongBei-SS opened 9 months ago
0
ERROR: BoundsError: attempt to access 0-element Vector{GeometryBasics.Point2{Float64}} at index [1]

#98 mzj0418 closed 9 months ago
4
Can't find border for cell and build polygon, no segmentation.csv

#97 hchen725 opened 10 months ago
0
Baysor v.0.6.2 Loaderror: No transcripts detected inside the segmented regions

#96 andynkili closed 9 months ago
2
Error when using prior segmentation

#95 kleejin opened 10 months ago
1
Baysor GeoJson output format question

#94 PoolLab opened 10 months ago
0
Inconsistent number of cells in the output files

#93 zsfrbkv closed 10 months ago
0
Precompilation warnings during Baysor run

#92 hchen725 opened 10 months ago
1
BAYSOR v0.6.2 ERROR: LoadError: MethodError: no method matching adjacency_list(::Vector{Any}; adjacency_type::Symbol, filter::Bool, return_tesselation::Bool)

#91 andynkili opened 10 months ago
4
Error with docker version v0.6.2

#90 andynkili opened 10 months ago
0
Container installation / singularity image

#89 sebgoti opened 10 months ago
1
Memory usage with huge datasets

#87 maximilian-heeg opened 11 months ago
6
LoadError: pca must have at least 3 components

#86 ankitbioinfo opened 11 months ago
1
Get stuck on 'Estimating local colors', memory use increases and freeze

#85 HaojiaWu closed 10 months ago
2
Baysor run stuck after 2D coordinates

#84 markutz556 closed 10 months ago
4
Baysor crashes with OutOfMemoryError() when prior segmentation column contains large integers

#83 pakiessling closed 10 months ago
2
ERROR: MethodError: no method matching boundary_polygons_from_grid(::Matrix{UInt32}; grid_step::Float64)

#82 sarahyk closed 10 months ago
8
How to deal with unassigned transcripts from prior segmentation

#81 jwrth closed 1 year ago
1
ERROR: ArgumentError: Package CSVFiles

#80 Dana162001 opened 1 year ago
2
Error: MethodError(Matrix{<:Unsigned}

#79 ccbvib opened 1 year ago
3
SparseArray recursion issue with baysor preview

#78 bhhlee closed 10 months ago
4
Error with v0.6.1

#77 ilyakorsunsky closed 1 year ago
1
Error when providing prior segmentation mask

#75 sebgoti closed 11 months ago
2