nf-core/lsa/cosine @ 0.0.0-0c7146d
Summary
Calculates the cosine similarity matrix between samples based on a gene expression matrix.
Get started
Add the following snippet to your workflow script to include this module.
include { LSA_COSINE } from 'nf-core/lsa/cosine'
License
MIT License
Process
Name
|
LSA_COSINE |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information, e.g. [ id:'test' ]. |
|---|---|
expression_matrix
file
|
CSV file containing the expression matrix. Rows should be features (genes) and columns should be samples. *.csv
|
Output
3 channels
#1
matrix
tuple
meta
map
|
Groovy Map containing sample information, e.g. [ id:'test' ]. |
|---|---|
*_matrix.csv
file
|
A square matrix (CSV) containing pairwise similarity scores. *_matrix.csv
|
#2
heatmap
tuple
meta
map
|
Groovy Map containing sample information, e.g. [ id:'test' ]. |
|---|---|
*_heatmap.png
file
|
A PNG image visualizing the similarity matrix as a heatmap. *_heatmap.png
|
#3
versions
versions.yml
file
|
File containing software versions. versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| lsa | Latent Semantic Analysis (LSA) package for R. | https://cran.r-project.org/web/packages/lsa/index.html |
| pheatmap | Pretty Heatmaps package for R. | https://cran.r-project.org/web/packages/pheatmap/index.html |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:14:37 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Flsa%2Fcosine/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/lsa/cosine/blobs/sha256:8d6f45df854b6db66382f36eaeb347a123862cb8da5e75ee7dd498b0d0009d26 |
| Size | 3.6 KB |
| Checksum | sha256:8d6f45df854b6db66382f36eaeb347a123862cb8da5e75ee7dd498b0d0009d26 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:28:06 (UTC) | 3 | 3.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:14:37 (UTC) | 4 | 3.6 KB |