pachterlab SpatialFeatureExperiment issues

pachterlab / SpatialFeatureExperiment

Extension of SpatialExperiment with sf

https://pachterlab.github.io/SpatialFeatureExperiment

Artistic License 2.0

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issues

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Issue with SpatialFeatureExperiment Object: Absolute Paths Referenced in the Object

#50 aasingh2 opened 1 week ago
6
Reimplement colFeatureData with `mcols`

#49 lambdamoses closed 2 weeks ago
0
Capacity Error with `readXenium()` Function and Issues Combining Samples Using `cbind()`

#48 aasingh2 opened 2 months ago
7
Could you add a function for plotting a reverse y-axis like GIOTTO? mirror or mirrorImg is not enough. Maybe a Mirror_Y_axis function To facilitate drawing and bridge the gap between different softwares

#47 huiyijiangling opened 2 months ago
1
Update acceptable Visium barcodes and allow an updated list to be given

#46 newmana closed 2 months ago
5
toSpatialFeatureExperiment() stopped working after updating to release version 1.6.1

#45 rcastelo closed 4 months ago
3
Backward compatibility with previous version of SpatRasterImage

#44 lambdamoses closed 4 months ago
0
cbind fails for more than 2 SFE objects when there're annotGeometries

#43 lambdamoses closed 6 months ago
0
add `readAkoya`

#42 alikhuseynov opened 6 months ago
0
Improve BioFormatsImage to store transform matrix

#41 lambdamoses closed 6 months ago
1
Split up SFE object or at least samples based on polygon contiguity

#40 lambdamoses closed 2 months ago
0
Allow minimum distance in distance based spatial graphs

#39 lambdamoses closed 4 months ago
0
Vignette on registering adjacent sections

#38 lambdamoses opened 6 months ago
0
Update `readXenium` for v2 output format

#37 lambdamoses closed 6 months ago
1
Change "sample_id = NULL" to all for multi samples and 1L for single …

#36 mingqizh closed 7 months ago
0
Slight misalignment of geometries and image after transformation of SFE object

#35 lambdamoses closed 5 months ago
0
Setter counterpart of `getImg`

#34 lambdamoses closed 4 months ago
0
Better support the complexity in sample relations

#33 lambdamoses opened 7 months ago
2
Optimize `sfc` affine transformation

#32 lambdamoses closed 5 months ago
1
Use geometry to decide which cells should have `sample_id` changed

#31 lambdamoses opened 7 months ago
0
Change `sample_id` with list of cell IDs

#30 lambdamoses opened 7 months ago
0
Merge method for SFE

#29 lambdamoses opened 7 months ago
3
Use geometries or bounding boxes to split up SFE object

#28 lambdamoses closed 2 months ago
4
Method to aggregate SFE object with spatial grid

#27 lambdamoses closed 2 months ago
0
Maybe: Change default to `withDimnames = FALSE` in setters

#26 lambdamoses closed 7 months ago
0
Better default `sample_id`

#25 lambdamoses closed 7 months ago
1
Get and set the primary `colGeometry`

#24 lambdamoses opened 7 months ago
2
Allow spatial subsetting with [ like in sf

#23 lambdamoses closed 4 months ago
0
Better error message when no spots/cells are left after cropping

#22 lambdamoses closed 7 months ago
0
Allow more than `sf` class in the Geometries

#21 lambdamoses opened 8 months ago
0
Supporting 3D cell segmentation

#20 lambdamoses opened 8 months ago
0
Rewrite my clunky `df2sf` to use `sfheaders`

#19 lambdamoses closed 8 months ago
1
Add `readMolKart` Resolve Bioscience

#18 alikhuseynov opened 10 months ago
0
Forthcoming changes in spdep break tests

#17 rsbivand closed 10 months ago
9
codex data

#16 Elena983 closed 8 months ago
2
support `crop()` for `rowGeometries`

#15 alikhuseynov closed 7 months ago
3
rowGeometry<- has never worked

#14 lambdamoses closed 1 year ago
1
`read10xVisiumSFE()` error when `data = "filtered"` for `style` arg

#13 alikhuseynov closed 1 year ago
2
`readVizgen()` and `readXenium()`

#12 alikhuseynov closed 8 months ago
79
Add readSeeker

#11 lambdamoses opened 1 year ago
0
Add readXenium

#10 lambdamoses closed 7 months ago
30
Add vignette on raster vector interaction

#9 lambdamoses opened 1 year ago
0
Refactor to remove the "missing" methods

#8 lambdamoses closed 1 year ago
1
Group functions on documentation page

#7 lambdamoses closed 1 year ago
0
Make cropping geometries optional in crop function

#6 lambdamoses closed 1 year ago
0
Use different bboxes to crop different samples in SFE object

#5 lambdamoses closed 1 year ago
0
tidySFE

#4 lambdamoses opened 1 year ago
0
convert Seurat to SFE and back

#3 alikhuseynov opened 1 year ago
15
Image pointers invalid when SFE object is loaded from rds

#2 lambdamoses closed 1 year ago
0
Wrong bbox used to crop images when multiple samples are present

#1 lambdamoses closed 1 year ago
0