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 | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:52:39 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Flsa%2Fcosine/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/lsa/cosine/blobs/sha256:f24ae87f88bd77f3fc752fff8201ab47e51dfd0286de87595131ae32ba8ccbd3 |
| Size | 3.6 KB |
| Checksum | sha256:f24ae87f88bd77f3fc752fff8201ab47e51dfd0286de87595131ae32ba8ccbd3 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:52:39 (UTC) | 1 | 3.6 KB | - |