Nextflow Registry | nf-core/scimap/spatiallda@0.0.0-0c7146d

nf-core/scimap/spatiallda @ 0.0.0-0c7146d

SpatialLDA uses an LDA based approach for the identification of cellular neighborhoods, using cell type identities.

spatial_neighborhoods scimap spatial_omics

Latest version: 0.0.0-0c7146d

Total downloads: 4

Source: nf-core/modules

Authors: @migueLib @chiarasch

Maintainers: @migueLib @chiarasch

SpatialLDA uses an LDA based approach for the identification of cellular neighborhoods, using cell type identities.

Add the following snippet to your workflow script to include this module.

include { SCIMAP_SPATIALLDA } from 'nf-core/scimap/spatiallda'

MIT License

Process

`Name`	`SCIMAP_SPATIALLDA`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`phenotyped` file	Phenotyped CSV file, it must contain the columns, sampleID, X, Y and Phenotype. `*.{csv}`

Output 4 channels

#1 versions

`versions.yml` file	File containing software versions `versions.yml`

#2 composition_plot tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.png` file	Plot with the motif composition and the cell type composition of motifs. `*.{png}`

#3 spatial_lda_output tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.csv` file	File with the motifs detected from SpatialLDA `*.{csv}`

#4 motif_location_plot tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.html` file	Plot with the locations of the motifs. `*.{html}`

Tool	Description	Homepage
scimap	Scimap is a scalable toolkit for analyzing spatial molecular data. The underlying framework is generalizable to spatial datasets mapped to XY coordinates. The package uses the anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. The Python-based implementation efficiently deals with large datasets of millions of cells.	https://scimap.xyz/

Version	0.0.0-0c7146d
Commit ID	0c7146d85582628b5d1034504702fa808632b1af
Release Date	08 Apr 2026 19:35:15 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fscimap%2Fspatiallda/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/scimap/spatiallda/blobs/sha256:42b83b359ad6890a41e073d9c356d5b548cc86e045aa8794911dec1761dce10a
Size	2.6 KB
Checksum	sha256:42b83b359ad6890a41e073d9c356d5b548cc86e045aa8794911dec1761dce10a
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-0c7146d	08 Apr 2026 19:35:15 (UTC)		4	2.6 KB