Tag: ALDEx2

Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…

Abstract In many high-throughput sequencing (HTS) studies, sample-to-sample variation in sequencing depth is not driven by variation in the scale (e.g., total size, microbial load, or total gene expression) of the underlying biological systems being measured but rather is driven by technical factors. Typically the technical variation is addressed using…

Sets of differentially abundant ASVs identified using ALDEx2 in each experimental variant described in Golebiewski et al. “Colonization of axenic beet by rhizosphere bacteria takes place in discreet phases regardless of bioinculation with next generation bioinoculant“. Files are in the tsv (tab separated values) format. Experimental variants are contained in…

Dynamics of immunogenicity at 6 months after BNT162b2 and CoronaVac vaccination From April 2021 to March 2022, we longitudinally followed 161 COVID-19 vaccinees who had received BNT162b2 (N = 121, 65.3% females) or CoronaVac vaccines (N = 40, 72.5% females). BNT162b2 vaccinees were younger compared to CoronaVac vaccinees [median (IQR) in years: 42 (29,…

Hello, I have a question about the complex study design in the R ALDEx2 package (bioconductor.org/packages/devel/bioc/vignettes/ALDEx2/inst/doc/ALDEx2_vignette.html#46_Complex_study_designs_and_the_aldexglm_module). My goal is to compare more than two groups (e.g. two or more treatments vs control). In a simple case with two groups, we use a vector with two groups: data(selex) #subset only the…

This is the development version of GenomicRanges; for the stable release version, see GenomicRanges. The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing…

How to export the result contents (analyzed part only) of clr function to the CSV file ? (The microbiota data) in R Aldex2 package 0 Hello, I am currently working on my ASV read count files to be normalized using R Aldex2 package, clr function. However, after I did clr…

hharder (Hannah Harder) March 1, 2023, 3:25pm 1 I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an…

excluded in the analysis. Solve optimization problems using an R interface to NLopt. The overall false discovery rate is controlled by the mdFDR methodology we In this formula, other covariates could potentially be included to adjust for confounding. depends on our research goals. W, a data.frame of test statistics. enter…

The colorectal cancer (CRC) screening program B-PREDICT is an invited two-stage screening project using a fecal immunochemical test (FIT) for initial screening followed by a colonoscopy for those with a positive FIT. Since the gut microbiome likely plays a role in the etiology of CRC, microbiome-based biomarkers in combination with…

turtle February 6, 2023, 5:30pm 1 Sorry for posting the same problem again.I’m having ALDEx2 plugin error. I tried the following code, conda install bioconductor-aldex2 -c defaults -c bioconda -c conda-forge conda install -c dgiguere q2-aldex2 But the error showing is, I was able to install ALDEx2 in R but…

Ms-Tai (Taiquitha T. Robins) July 19, 2022, 2:49am #1 Plugin error from aldex2:An error was encountered while running ALDEx2 in R (return code 1), please inspect stdout and stderr to learn more.Debug info has been saved to /tmp/qiime2-q2cli-err-4j7_h2at.log lizgehret (Liz Gehret) July 19, 2022, 5:15pm #2 Hi @Ms-Tai, Please include…

DOI: 10.18129/B9.bioc.ALDEx2     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ALDEx2. Analysis Of Differential Abundance Taking Sample Variation Into Account Bioconductor version: 3.9 A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard…