drighelli SpatialExperiment issues

drighelli / SpatialExperiment

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allow additional image extensions

#160 andrewGhazi opened 3 weeks ago
0
Allow additional SpatialImage file extensions

#159 andrewGhazi opened 3 weeks ago
2
TreeSummarizedExperiment support

#158 TuomasBorman opened 1 month ago
12
Basic import of seqFISH from Spatial Genomics genePS into SpatialExperiment

#157 methornton closed 3 months ago
7
Remove all spatialData-related documentation, code & comments

#156 HelenaLC opened 5 months ago
0
Deprecate read10xVisium()

#155 HelenaLC closed 5 months ago
2
#151

#154 HelenaLC closed 5 months ago
0
Update GitHub Actions for Bioc version 3.19

#153 lmweber closed 5 months ago
0
Version bumps from Bioc 3.19 release

#152 lmweber closed 5 months ago
0
Unexpected error when `spe$sample_id` is a factor

#151 Nick-Eagles opened 6 months ago
1
Potential new`.parquet` format for `tissue_position` of VisiumHD might trigger issues for `read10xVisium`

#150 boyiguo1 closed 5 months ago
8
Update README.md

#149 federicomarini closed 7 months ago
5
Merging version bumps from last Bioc release and updating GHA

#148 lmweber closed 8 months ago
4
error adding image

#147 alfonsosaera opened 10 months ago
7
spatial proteomics data to SPE

#146 cathalgking opened 10 months ago
1
Possibility of adding `in_filtered` to read10xVisium(data = "raw")

#145 lcolladotor closed 1 month ago
7
add functions readXeniumSPE(), readCosmxSPE(), readMerscopeSPE(), and example data

#144 estellad opened 1 year ago
9
feat: check existence instead of equality for colnames of imgData

#143 senbaikang opened 1 year ago
22
More flexible colnames of `imgData`

#142 senbaikang opened 1 year ago
0
Deprecate BumpyMatrix functionality for molecule-based data

#141 lmweber opened 1 year ago
2
Move DropletUtils to Suggests to reduce dependencies

#140 lmweber closed 1 year ago
3
Dependencies

#139 ellispatrick closed 1 year ago
4
Bioc release version bumps and GitHub Actions update

#138 lmweber closed 1 year ago
8
Bugfix for tissue positions read in incorrect order (release version)

#137 lmweber closed 1 year ago
1
Fix https://github.com/drighelli/SpatialExperiment/issues/135 -- thou…

#136 lcolladotor closed 1 year ago
4
read10xVisium() in version 1.7.1 (and now 1.8.0) creates a dangerous silent error by mismatching tissue positions across multiple samples

#135 lcolladotor closed 1 year ago
10
Fix image file path handling in Windows checks

#134 lmweber closed 1 year ago
2
Error building vignette in windows

#133 drighelli closed 1 year ago
1
Error in creating `RemoteSpatialImage`

#132 lgeistlinger closed 2 years ago
3
SpatialImage doc questions

#131 lgeistlinger opened 2 years ago
2
`withDimnames` argument in `spatialCoords` getter & setter

#130 HelenaLC closed 2 years ago
1
Updating documentation

#129 drighelli closed 2 years ago
0
`cbind`: unique/duplicated `colnames`are left asis/made unique; `read10xVisium`: keep barcodes as `colData`; `spatialCoords/<-`: `withDimnames` argument

#128 HelenaLC opened 2 years ago
2
restructure `imgData` with flexible `metadata`

#127 HelenaLC opened 2 years ago
0
move `read10xVisium` to `TENxIO`

#126 HelenaLC opened 2 years ago
27
Version bump for Bioc builders

#125 lmweber closed 2 years ago
1
Version bump and GitHub Actions

#124 lmweber closed 2 years ago
3
`read10xVisium` tries to add `outs` to my paths

#123 LTLA opened 2 years ago
3
Rebased the SpatialImage classes on Annotated.

#122 LTLA closed 2 years ago
1
Could imgData also store other image classes?

#121 lgeistlinger opened 2 years ago
1
imgData slot restrictions

#120 lgeistlinger opened 2 years ago
5
How to SpatialFeaturePlot for Aggregated Samples?

#119 chancharikmitra opened 2 years ago
2
Error when uploading Visium data

#118 martina-morchio closed 2 years ago
5
add $ method in SpatialExperiment, closes #107

#117 LiNk-NY closed 2 years ago
6
Latest Spaceranger 2.0 output structure change breaks `read10xVisium`

#116 raysinensis opened 2 years ago
1
Convert Seurat to SpatialExperiment

#115 MarcElosua opened 2 years ago
3
Dependency stack

#114 lgeistlinger opened 2 years ago
4
Dim,stored spatial image method

#113 HelenaLC closed 2 years ago
2
`dim,StoredSpatialImage-method` should use `magick::image_info(img)` if raster is not loaded

#112 LTLA closed 2 years ago
3
`?imgRaster` should offer a choice between the SpatialExperiment and SpatialImage methods

#111 LTLA opened 2 years ago
5