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SQMtools  

Analyze Results Generated by the 'SqueezeMeta' Pipeline
View on CRAN: Click here


Download and install SQMtools package within the R console
Install from CRAN:
install.packages("SQMtools")

Install from Github:
library("remotes")
install_github("cran/SQMtools")

Install by package version:
library("remotes")
install_version("SQMtools", "1.7.2")



Attach the package and use:
library("SQMtools")
Maintained by
Fernando Puente-Sánchez
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-03-20
Latest Update: 2025-06-14
Description:
'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.
How to cite:
Fernando Puente-Sánchez (2023). SQMtools: Analyze Results Generated by the 'SqueezeMeta' Pipeline. R package version 1.7.2, https://cran.r-project.org/web/packages/SQMtools. Accessed 28 Jul. 2026.
Previous versions and publish date:
(2026-07-09 08:25), 1.6.2 (2023-03-20 11:30), 1.6.3 (2023-09-18 11:00), 1.7.0 (2025-03-31 23:10), 1.7.1 (2025-06-04 11:20), 1.7.2 (2025-06-14 08:30)
Other packages that cited SQMtools R package
View SQMtools citation profile
Other R packages that SQMtools depends, imports, suggests or enhances
Complete documentation for SQMtools
Functions, R codes and Examples using the SQMtools R package
Full SQMtools package functions and examples
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