Description

NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data. NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes. Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

rcc_files:file

List of RCC files for all samples, which are direct outputs from NanoString runs

*.RCC

meta2:map

Groovy Map containing file information e.g. [ id:‘test_samplesheet’ ]

sample_sheet:file

Comma-separated file with 3 columns: RCC_FILE, RCC_FILE_NAME, and SAMPLE_ID

*.csv

Output

name:type
description
pattern

normalized_counts

meta:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

normalized_counts.tsv:file

Tab-separated file with gene normalized counts for the samples

normalized_counts.tsv

normalized_counts_wo_HK

meta:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

normalized_counts_wo_HKnorm.tsv:file

Tab-separated file with gene normalized counts for the samples, without housekeeping genes.

normalized_counts_wo_HKnorm.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

NACHO
GPL-3.0

R package that uses two main functions to summarize and visualize NanoString RCC files, namely: `load_rcc()` and `visualise()`. It also includes a function `normalise()`, which (re)calculates sample specific size factors and normalises the data. For more information `vignette("NACHO")` and `vignette("NACHO-analysis")`

args_id: $args
github.com/mcanouil/NACHO cran.r-project.org/web/packages/NACHO/vignettes/NACHO 10.1093/bioinformatics/btz647
included in
nanostring
maintainer
Github user alanmmobbs93
get in touch
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