Tag: phyloseq

Zea mays genotype influences microbial and viral rhizobiome community structure

Oburger E, Schmidt H. New methods to unravel rhizosphere processes. Trends Plant Sci. 2016;21:243–55. Article  CAS  PubMed  Google Scholar  Rout ME, Southworth D. The root microbiome influences scales from molecules to ecosystems: the unseen majority. Am J Bot. 2013;100:1689–91. Article  PubMed  Google Scholar  Pratama AA, Terpstra J, de Oliveria ALM,…

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Survey of the infant male urobiome and genomic analysis of Actinotignum spp.

Wolfe, A. J. et al. Evidence of uncultivated bacteria in the adult female bladder. J. Clin. Microbiol. 50, 1376–1383 (2012). Article  PubMed  PubMed Central  Google Scholar  Hilt, E. E. et al. Urine is not sterile: Use of enhanced urine culture techniques to detect resident bacterial flora in the adult female…

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r-bioc-phyloseq 1.22.3-1

/usr/ root:root 0o755 /usr/lib/ root:root 0o755 /usr/lib/R/ root:root 0o755 /usr/lib/R/site-library/ root:root 0o755 /usr/lib/R/site-library/phyloseq/ root:root 0o755 /usr/lib/R/site-library/phyloseq/CITATION text/plain root:root 0o644 606 bytes /usr/lib/R/site-library/phyloseq/data/ root:root 0o755 /usr/lib/R/site-library/phyloseq/data/datalist text/plain root:root 0o644 44 bytes /usr/lib/R/site-library/phyloseq/data/enterotype.RData application/x-xz root:root 0o644 190.7 KB /usr/lib/R/site-library/phyloseq/data/esophagus.RData application/x-xz root:root 0o644 1.8 KB /usr/lib/R/site-library/phyloseq/data/GlobalPatterns.RData application/x-xz root:root 0o644 425.4 KB /usr/lib/R/site-library/phyloseq/data/soilrep.RData application/x-xz root:root 0o644 104.9 KB /usr/lib/R/site-library/phyloseq/DESCRIPTION text/plain…

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Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article  ADS  CAS  PubMed  Google Scholar  Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….

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Online metagenomics training (free) in April

Free Cloud-SPAN course on METAGENOMICS 11-21 April 2023  Join our experts for this free online module! We welcome environmental scientists who would like to use high performance computing for metagenomics analysis, or anyone with an interest in metagenomics to register. No previous experience of the command line or HPC is…

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Bioconductor – DESeq2 (development version)

DOI: 10.18129/B9.bioc.DESeq2   This is the development version of DESeq2; for the stable release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: Development (3.19) Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

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Solved Use phyloseq for the question. Here is the

Use phyloseq for the question. Here is the dataset: [1] “BW1_sub_R1_trimmed.fq” “BW1_sub_R2_trimmed.fq” [3] “BW2_sub_R1_trimmed.fq” “BW2_sub_R2_trimmed.fq” [5] “filtered” “R10_sub_R1_trimmed.fq” [7] “R10_sub_R2_trimmed.fq” “R11_sub_R1_trimmed.fq” [9] “R11_sub_R2_trimmed.fq” “R11BF_sub_R1_trimmed.fq” [11] “R11BF_sub_R2_trimmed.fq” “R12_sub_R1_trimmed.fq” [13] “R12_sub_R2_trimmed.fq” “R1A_sub_R1_trimmed.fq” [15] “R1A_sub_R2_trimmed.fq” “R1B_sub_R1_trimmed.fq” [17] “R1B_sub_R2_trimmed.fq” “R2_sub_R1_trimmed.fq” [19] “R2_sub_R2_trimmed.fq” “R3_sub_R1_trimmed.fq” [21] “R3_sub_R2_trimmed.fq” “R4_sub_R1_trimmed.fq” [23] “R4_sub_R2_trimmed.fq” “R5_sub_R1_trimmed.fq” [25] “R5_sub_R2_trimmed.fq” “R6_sub_R1_trimmed.fq” [27] “R6_sub_R2_trimmed.fq”…

Continue Reading Solved Use phyloseq for the question. Here is the

Solved Use phyloseq for this question. Here is the dataset:

Use phyloseq for this question. Here is the dataset: [1] “BW1_sub_R1_trimmed.fq” “BW1_sub_R2_trimmed.fq” [3] “BW2_sub_R1_trimmed.fq” “BW2_sub_R2_trimmed.fq” [5] “filtered” “R10_sub_R1_trimmed.fq” [7] “R10_sub_R2_trimmed.fq” “R11_sub_R1_trimmed.fq” [9] “R11_sub_R2_trimmed.fq” “R11BF_sub_R1_trimmed.fq” [11] “R11BF_sub_R2_trimmed.fq” “R12_sub_R1_trimmed.fq” [13] “R12_sub_R2_trimmed.fq” “R1A_sub_R1_trimmed.fq” [15] “R1A_sub_R2_trimmed.fq” “R1B_sub_R1_trimmed.fq” [17] “R1B_sub_R2_trimmed.fq” “R2_sub_R1_trimmed.fq” [19] “R2_sub_R2_trimmed.fq” “R3_sub_R1_trimmed.fq” [21] “R3_sub_R2_trimmed.fq” “R4_sub_R1_trimmed.fq” [23] “R4_sub_R2_trimmed.fq” “R5_sub_R1_trimmed.fq” [25] “R5_sub_R2_trimmed.fq” “R6_sub_R1_trimmed.fq” [27] “R6_sub_R2_trimmed.fq”…

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Bioconductor – phyloseq

DOI: 10.18129/B9.bioc.phyloseq     Handling and analysis of high-throughput microbiome census data Bioconductor version: Release (3.6) phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Author: Paul J. McMurdie <joey711 at gmail.com>, Susan Holmes <susan at stat.stanford.edu>, with…

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Phyloseq Object Sample Names Error

### Error Message Overview The error message `Error in validObject(.Object) : invalid class “phyloseq” object: Component sample names do not match. Try sample_names()` indicates that there is an issue with the sample names in the `phyloseq` object being created. The error suggests that the sample names provided for the OTU…

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Phage therapy minimally affects the water microbiota in an Atlantic salmon (Salmo salar) rearing system while still preventing infection

Shreiner, A. B., Kao, J. Y. & Young, V. B. The gut microbiome in health and in disease. Curr. Opin. Gastroenterol. 31, 69–75. doi.org/10.1097/Mog.0000000000000139 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  Selber-Hnatiw, S. et al. Human gut microbiota: Toward an ecology of disease. Front. Microbiol. 8, 1265. doi.org/10.3389/fmicb.2017.017E5 (2017)….

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Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria

Isolation of phyllosphere isolates All bacterial strains were isolated in June 2021 from the flag leaves of four wheat cultivars (Sheriff, Heerup, Rembrandt and Kvium) grown in an experimental field in Høje Taastrup, near Copenhagen, Denmark. Wheat flag leaves were picked, pooled, and either washed or blended prior to dilution…

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Large qiime2 table (107 gb) to phyloseq

Large qiime2 table (107 gb) to phyloseq 0 Hello, I’m currently engaged in a microbiome meta-analysis and have combined a dada2 table involving data from 83 different studies. The file size of this merged table is 107GB. However, I’m encountering difficulties reading this file in R to conduct statistical analyses….

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Phyloseq sample data error: non-zero dimensions?

Phyloseq sample data error: non-zero dimensions? 0 I’m trying to filter/extract out individuals from the genetic data that has a gut gene data. However, when I tried to run the phyloseq, it gave me an error that my phyloseq object (sample_data) needs to be non-zero dimensions. filt_physeq <- subset_samples(gut_phyloseq, sample_names(gut_phyloseq)…

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Error when making phyloseq object

Hi, I am having issues when loading data into my phyloseq object. I have read the other posts here about similar issues and tried using those tactics but I seem to have a different issue here. Any ideas how to troubleshoot this? I am attaching screenshots of the 3 tables…

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Online metagenomics training (free) in November 2023

Free Cloud-SPAN course on METAGENOMICS Monday 6th to Friday 24th November 2023. Join our experts for this free online workshop! We welcome environmental scientists who would like to use high performance computing for metagenomics analysis, or anyone with an interest in metagenomics to register. No previous experience of the command…

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Bacterial networks in Atlantic salmon with Piscirickettsiosis

Verschuere, L., Rombaut, G., Sorgeloos, P. & Verstraete, W. Probiotic bacteria as biological control agents in aquaculture. Microbiol. Mol. Biol. Rev. 64(4), 655–671 (2000). Article  CAS  PubMed  PubMed Central  Google Scholar  Gomez, G. D. & Balczar, J. L. A review on the interactions between gut microbiota and innate immunity of…

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Does ASVs IDs from dada2 have specific taxonomic assignments?

Does ASVs IDs from dada2 have specific taxonomic assignments? 1 Hello Community, I’m trying to subset matrices of ASVs’s associations that were produced from 2 different phyloseq objects. For downstream analysis I need to subset the square matrices in a way that the exactly same taxa are contained in both…

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Phyloseq and ASV names between datasets

Hi, I ran DADA2 on 3 16S-datasets , what went well. Then, I imported the output files to phyloseq in R to create some abundances tables, graphs etc. My problem is to correlate the ASV names between the 3 abundance tables. I mean, each ASV will be named ASV1, ASV2…

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q2-dada2 -p-pooling-method TRUE for large number of samples then move to R – User Support

Eman (Eman Khalaf) October 8, 2023, 4:50pm 1 Hi, I have many samples (~650) sequenced by PacBio platform. RStudio can not process dada function due to the memory limit of the software. The total size of the samples is 30 GB and I need to use pool=TRUE parameter. So, I…

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gmteunisse/Fantaxtic source: R/collapse_taxa.R

#’ Subset a phyloseq object to a set of taxa. #’ #’ This function takes a phyloseq object and a list of taxon ids to be kept, #’ and discards or merges all other taxa. #’ #’ @details #’ This function is essentially a wrapper around \link[phyloseq]{prune_taxa} and #’ \link[phyloseq]{merge_taxa}….

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gmteunisse/Fantaxtic source: R/top_taxa.R

#’ Get the most abundant taxa from a phyloseq object #’ #’ This function identifies the top \eqn{n} taxa in a phyloseq object. Users specify the #’ summary statistic that is used to rank the taxa, e.g. \code{sum}, \code{mean} or #’ \code{median}. Furthermore, it is possible to add one or…

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Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing

Soil incubation and cell extraction Approximately 3 kg of unmanaged marginal soil (pH 8) was collected from the Pacific Northwest National Laboratory field site in Prosser, Washington (46° 15′ 04″ N and 119° 43′ 43″ W) [23], homogenized, sieved (4 mm mesh size), and stored at 4 °C until further processing. Probe specific…

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The succession of epiphytic microalgae conditions fungal community composition: how chytrids respond to blooms of dinoflagellates

Jones EBG, Suetrong S, Sakayaroj J, Bahkali AH, Abdel-Wahab MA, Boekhout T, et al. Classification of marine Ascomycota, Basidiomycota, Blastocladiomycota and Chytridiomycota. Fungal Divers. 2015;73:1–72. Article  Google Scholar  Van den Wyngaert S, Ganzert L, Seto K, Rojas-Jimenez K, Agha R, Berger SA, et al. Seasonality of parasitic and saprotrophic zoosporic…

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Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast

Rubin, S., Parr, T., Da Costa, L. & Friston, K. Future climates: Markov blankets and active inference in the biosphere. J. R. Soc. Interface 17, 20200503 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Cantonati, M. et al. Characteristics, main impacts, and stewardship of natural and artificial freshwater environments: Consequences…

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FROGS analysis and Phyloseq – troubleshooting

mcornet September 20, 2023, 10:28am 1 How can I suppress uniditified ITS sequences in FROGS for Phyloseq analysis jennaj September 20, 2023, 5:51pm 2 Hello @mcornet I don’t think that FROGS has been wrapped for Galaxy yet, but could be wrong! Where are you using the tool? If you can…

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Software Compatibility Issue Between phyloseq and lme4 Packages

Hi, I’ve encountered a rather peculiar software issue involving the phyloseq package and the lme4 package when analyzing longitudinal microbiome data. Below, please find a reproducible example that triggers the error: First, when I run the mixed effects model code provided by lme4, it works perfectly: data(“sleepstudy”, package = “lme4”)…

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Effects of oxygen availability on mycobenthic communities of marine coastal sediments

LaRowe, D. E. et al. The fate of organic carbon in marine sediments—New insights from recent data and analysis. Earth-Sci. Rev. 204, ARTN 103146. doi.org/10.1016/j.earscirev.2020.103146 (2020). Article  CAS  Google Scholar  Orsi, W. D. et al. Carbon assimilating fungi from surface ocean to subseafloor revealed by coupled phylogenetic and stable isotope…

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bioconductor – Issue with downloading phyloseq, in R 4.3.1

I am trying to download the package phyloseq in R 4.3.1 to complete an analysis for my master’s thesis on my MacOS M1. when I input the bioconductor code for installing the package phyloseq: if (!require(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“phyloseq”) I get the following (very long) error (screenshot because…

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Plasmodium falciparum population structure inferred by msp1 amplicon sequencing of parasites collected from febrile patients in Kenya | Malaria Journal

WHO. World malaria report 2021. Geneva: World Health Organization; 2021. Google Scholar  Kenya Demographic and Health Survey. 2021 Kenya Malaria Indicator Survey. Nairobi, Kenya, 2021. Anderson TJC, Haubold B, Williams JT, Estrada-franco JG, Richardson L, Mollinedo R, et al. Microsatellite markers reveal a spectrum of population structures in the malaria…

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Cloud-SPAN course: Metagenomics | Software Sustainability Institute

Cloud-SPAN will host a free course on metagenomics from Monday 6, until Friday 24 November 2023. The course is aimed at environmental scientists who would like to use high performance computing for metagenomics analysis or anyone interested in metagenomics. No previous experience of the command line or HPC is required. The deadline to…

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Effects of host species on microbiota composition in Phlebotomus and Lutzomyia sand flies | Parasites & Vectors

Maroli M, Feliciangeli MD, Bichaud L, Charrel RN, Gradoni L. Phlebotomine sandflies and the spreading of leishmaniases and other diseases of public health concern. Med Vet Entomol. 2013;27:123–47. CAS  PubMed  Google Scholar  Akhoundi M, Kuhls K, Cannet A, Votypka J, Marty P, Delaunay P, et al. Historical overview of the…

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r – otu_table from phyloseq object does not have correct abundance: all asv are “0” for specific group of samples

I have QIIME2 outputs (feature table, tree, taxonomy, and metadata) that I’ve imported into R using qiime2R (v. 0.99.6) ‘qza_to_phyloseq’ to create a phyloseq object. My QIIME feature table shows reasonable values for ASV abundance across all samples (n=16; feature table available upon request). Problem: The otu_table the ASV values…

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Neighborhood socioeconomic status is associated with low diversity gut microbiomes and multi-drug resistant microorganism colonization

Buettgens, M., Blavin, F. & Pan, C. The affordable care act reduced income inequality in the US. Health Aff. 40, 121–129 (2021). Article  Google Scholar  Chen, E. & Miller, G. E. Socioeconomic status and health: mediating and moderating factors. Annu. Rev. Clin. Psychol. 9, 723–749 (2013). Article  PubMed  Google Scholar …

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Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia

Dadgostar, P. Antimicrobial resistance: Implications and costs. Infect. Drug Resistance 12, 3903–3910 (2019). Article  CAS  Google Scholar  Rosenblatt-Farrell, N. The landscape of antibiotic resistance. Environ. Health Perspect. 117, A244–A250 (2009). Article  PubMed  PubMed Central  Google Scholar  Roberts, S. C. & Zembower, T. R. Global increases in antibiotic consumption: a concerning…

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Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales

Romans, B. W. & Graham, S. A. A deep-time perspective of land–ocean linkages in the sedimentary record. Annu. Rev. doi.org/10.1146/annurev-marine-121211-172426 (2013). Article  Google Scholar  Smith, S. V. & Hollibaugh, J. T. Coastal metabolism and the ocean organic carbon balance. Rev. Geophys. 31, 75–89 (1993). Article  ADS  Google Scholar  Bauer, J….

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Sample ID in feature table and meta data not in order – Other Bioinformatics Tools

A. I got this error (below) for this code physeq <- qza_to_phyloseq( features = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/dada2_table_16S.qza”, tree = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/phylogeny-align-to-tree-mafft-fasttree/rooted_tree.qza”, taxonomy = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/taxonomy.qza”, metadata = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/metadata16S.tsv” )Error in validObject(.Object) : invalid class “phyloseq” object:Component sample names do not match.Try sample_names() As I was trying to look into detail, this was the error,…

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Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population | BMC Gastroenterology

Study populations Between 2015 and 2019, stool samples and data were collected from 219 IBD subjects (CD or UC) attending the Internal Medicine Clinics, King Fahd Hospital of the University, Al-Khobar and King Fahad Hospital, Alhafof, Saudi Arabia. Diagnosis of IBD was based on endoscopy (for CD) or colonoscopy (for…

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Diversity and potential plant growth promoting capacity of seed endophytic bacteria of the holoparasite Cistanche phelypaea (Orobanchaceae)

Bodelier, P. L. E. & Dedysh, S. N. Microbiology of wetlands. Front. Microbiol. 4, 79. doi.org/10.3389/fmicb.2013.00079 (2013). Article  PubMed  PubMed Central  Google Scholar  Tebbe, D. A. et al. Seasonal and zonal succession of bacterial communities in North Sea salt marsh sediments. Microorganisms 10(5), 859. doi.org/10.3390/microorganisms10050859 (2022). Article  CAS  PubMed  PubMed…

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Scientist (Virologist, NGS, Bioinformatics) job with Reckitt

Description Want to be at the cutting edge? As Scientist (Virologist, NGS, Bioinformatics) at Reckitt, you’ll have the freedom to turn ground-breaking technologies into consumer healthcare solutions. Scientist (Virologist, NGS, Bioinformatics) Montvale, NJ Competitive Salary & excellent benefits package A key role in a multinational team, you’ll be responsible for…

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Differential contribution of nitrifying prokaryotes to groundwater nitrification

Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018;16:263–76. Article  CAS  PubMed  Google Scholar  Koch H, van Kessel MAHJ, Lücker S. Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biotechnol. 2018;103:177–89. Article  PubMed  PubMed Central  Google Scholar  Lehtovirta-Morley LE Ammonia oxidation: ecology,…

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Export phyloseq tree to qiime2 – User Support

Nelly (Nelly) July 4, 2023, 12:27pm 1 Hi,I have a Phyloseq object and I am interested in exporting the Phyloseq tree to QIIME2. Since I created the Phyloseq object from WGS data, I wasn’t able to take the sequences and construct a phylogenetic tree based on the sequences. Instead, I…

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How to add a refseq() slot to a MAG based phyloseq object ?

How to add a refseq() slot to a MAG based phyloseq object ? 0 Hello, I was asked to build a phyloseq object from some metagenome assembled genomes that I built. By far I have created a tax_table() slot from the classification of the MAGs using GTDB-Tk, a out_table() that…

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2D PCoA plot error qiime2 – Technical Support

Han_Do (Han Do) June 28, 2023, 7:43pm 1 Hi everyone, I wanted to make a 2D PCoA plots similar to the one below. I can’t find any other codes than these. So, I used it and it gave me error. (qiime2-2023.5) hando@Cinderellas-MacBook-Pro AlphaDiversity_FS % qiime tools export –output-dir exported unweighted_unifrac_pcoa_results.qzamake_2d_plots.py…

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Rarefaction curve of microbiome study

I don’t know why my rarefaction curve for most samples does not reach saturation. Please how can I improve te curve? The curve does not look like most rarefaction curves I see in publications, Please help and I am relatively new to microbiome study. Below is the code I used:…

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r – RStudio plot window won’t finish loading and/or won’t properly load my plot

I’m trying to create a plot showing the abundance of ASVs within control vs true samples. This isn’t an issue with the code since I’ve used it before and it was just working yesterday, but I’ll include it here: # Starting from a phyloseq object called “noMitoChloroMock_physeq” # Set control…

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Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria) | Parasites & Vectors

Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, et al. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018;16:410–22. doi.org/10.1038/s41579-018-0029-9. Article  CAS  PubMed  Google Scholar  Blaxter M. Counting angels with DNA. Nature. 2003;421:122–3. doi.org/10.1038/421122a. Article  CAS  PubMed  Google Scholar  Cordier T, Alonso-Sáez L, Apothéloz-Perret-Gentil L, Aylagas…

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r – plot_ordination function of phyloseq plots shapes ‘double’ within itself

I’m analysing NGS data using the phyloseq package. I want to create a PCoA (Bray-curtis DM) plot using following code: ord_bc_pcoa<-ordinate(physeq,method=”PCoA”, distance=”bray”) pcoa_plot_1<-plot_ordination(physeq,ord_bc_pcoa,color=”variable1″, shape=”variable2″) + geom_point(size=4) + scale_color_manual(values = c(“var1X”=”red”,”var1Y”=”#55BE25″,”var1Z”=”blue”)) + scale_shape_manual(values = c(“var2A”=0,”var2B”=2,”var2C”=3,”var2D”=4,”var2D”=5,”var2E”=6,”varF”=7,”var2G”=8)) + ggtitle(“title1”) pcoa_plot_1 In the resulting plot, the shapes look like this: As you can see,…

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Query regarding phyloseq object construct with QIIME output

Query regarding phyloseq object construct with QIIME output 0 @6d5973d2 Last seen 15 hours ago India I used qiime pipeline to analyze 16s amplicon sequencing data now I want to take those outputs into r studio with the help of phyloseq package and want to create phyloseq object that’s how…

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Remove duplicate genera in DEseq output?

Hi all, I successfully ran DESeq2, though I am looking for differential abundance of microbial genera, not gene expression. However, duplicate genera (assigned to different species in my taxa table) are listed out and numbered instead of collapsing. I would like to collapse duplicate genera. Here is what I ran…

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Introduction to R for Microbiome Data

Abubucker, Sahar, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, and Curtis Huttenhower. 2012. Metabolic reconstruction for metagenomic data and its application to the…

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PCoA results differ between r and QIIME even when using QIIME-produced matrix – General Discussion

naltmank (Noam Altman-Kurosaki) May 15, 2023, 3:21pm 1 Hi there, Not to add to the glut of questions regarding PCoA outputs on QIIME vs R, but I couldn’t find one that addresses the issue I’m having. For some background, I have multiple distance matrices that I’ve produced using phyloseq, rbiom,…

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I keep getting error with the use of ggplot 2 – General

Greetings! I’ve been trying to make a diferential graphic with the package microbiota process everything seems ok, but when I wanna do a graphic by time i just kept getting error.I’m working from phyloseq object converted to mpse one. I think maybe my group by time is the problem here…

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Reckitt hiring Scientist (Virologist, NGS, Bioinformatics) in Montvale, New Jersey, United States

DescriptionWant to shake things up? As Scientist (Virologist, NGS, Bioinformatics) at Reckitt, you’ll have the freedom to explore disruptive technologies and see just how far you can take them.Scientist (Virologist, NGS, Bioinformatics)Montvale, NJCompetitive Salary & Excellent Benefits PackageFinding health solutions that make a difference to consumers’ lives is a constant…

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Bioconductor – biomformat – rbiom: Read/Write, Transform, and Summarize ‘BIOM’ Data

DOI: 10.18129/B9.bioc.biomformat     This package is for version 3.8 of Bioconductor; for the stable, up-to-date released release, checkbiomformat. An interface package for the BIOM file format Bioconductor version: 3.8 This is an R packages for interfacing from the BIOM format. This package inclusive bottom tools since reading biom-format files,…

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Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection

Global tuberculosis report 2020. (Geneva: World Health Organization; 2020. Licence: CC BY-NC-SA 3.0 IGO). Acuña-Villaorduna, C. et al. Intensity of exposure to pulmonary tuberculosis determines risk of tuberculosis infection and disease. Eur. Respir. J. 51, 1. doi.org/10.1183/13993003.01578-2017 (2018). Article  Google Scholar  Reichler, M. R. et al. Duration of exposure among…

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visualization output Tax4fun2 – STAMP?

visualization output Tax4fun2 – STAMP? 1 Hi everyone, I have used Tax4fun2 for predicting functional, following a tutorial I found online: rpubs.com/Tona_MP/pt2_Curso I have now 2 text files, one “functional_prediction.txt”, and one “pathway_prediction.txt”, which look as follows: functional prediction txt file: KO IAM01.T1 IAM01.T7 IAM02.T1 IAM02.T7 [for all samples] description…

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Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon | Parasites & Vectors

Gao H, Cui C, Wang L, Jacobs-Lorena M, Wang S. Mosquito microbiota and implications for disease control. Trends Parasitol. 2020;36:98–111. Article  PubMed  Google Scholar  Scolari F, Casiraghi M, Bonizzoni M. Aedes spp. and their microbiota: a review. Front Microbiol. 2019;10:2036. Article  PubMed  PubMed Central  Google Scholar  Steven B, Hyde J,…

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Gut taste receptor type 1 member 3 is an intrinsic regulator of Western diet-induced intestinal inflammation | BMC Medicine

Study design The objective of the study was to evaluate the influence of long-term WD intake on intestinal inflammation and investigate possible mechanisms by which WD intake could affect IBD development. To this end, mice were fed normal diet (ND) or WD for 10 weeks, and bowel inflammation was evaluated through…

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what are important packages – General

I keep getting some errors when trying to get packages, for example, phyloseq packageSeems like something is missing in the system if(!requireNamespace(“BiocManager”, quietly = TRUE))install.packages(“BiocManager”)BiocManager::install(“phyloseq”) /usr/bin/ld: cannot find -llapack/usr/bin/ld: cannot find -lblascollect2: error: ld returned 1 exit statusmake: *** [/usr/share/R/share/make/shlib.mk:10: igraph.so] Error 1ERROR: compilation failed for package ‘igraph’ removing ‘/home/alla/R/x86_64-pc-linux-gnu-library/4.2/igraph’Warning…

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Phyloseq Introduction and Import | Loading Microbiome Data

Phyloseq and Microbiome analyzed in R Data Import and Exploration There are a number of packages advanced in R that make microbiome analysis easy and erzeugt greater figures. At is by times an lot of overlap between this analyse and QIIME – and the choice is yours. Personally I consider…

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Previously uncharacterized rectangular bacterial structures in the dolphin mouth

To maximize reproducibility, a list of the reagents and resources used in this study, as well as their source and identifier, is provided in Supplementary Table 5. Experimental model and subject details Oral swab samples were obtained from bottlenose dolphins (Tursiops truncatus) managed by the U.S. Navy MMP Biosciences Division, Space…

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Characterization of rumen microbiome and metabolome from oro-esophageal tubing and rumen cannula in Holstein dairy cows

All experimental procedures were conducted at the University of Illinois at Urbana-Champaign and followed protocols approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Illinois at Urbana-Champaign under protocol number 17172. All ARRIVE, and IACUC guidelines and regulations were followed during the entire duration of…

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Expanding known viral diversity in the healthy infant gut

Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Milani, C. et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol. Mol. Biol. Rev. 81, e00036-17…

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phyloseq error

phyloseq error 0 Hi There I am using phyloseq and I get the following error message OTU = otu_table(otumat, taxa_are_rows=TRUE) Error in validObject(.Object) : invalid class “otu_table” object: Non-numeric matrix provided as OTU table. Abundance is expected to be numeric. Could you please advise what am I doing wrong and…

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Page Not Found – Posit Community

Sign Up Log In Log In Popular I am getting this error again and again of crash previous session.Posit Cloud graph with 2 Y axisGeneral How to make read_csv smarter at infering column types?tidyverse How to resolvw a problem to RstudioGeneral Why the correlation coefficient of Kendall’s Tau is small…

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Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods | Environmental Microbiome

O’Neill J. The Review on Antimicrobial Resistance—tackling drug-resistant infections globally: final report and recommendations. 2016. Murray CJ, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet. 2022;399:629–55. Article  CAS  Google Scholar  Laxminarayan R….

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does anyone how to create rarefaction curves from a phyloseq object?

does anyone how to create rarefaction curves from a phyloseq object? 0 @aa1632d5 Last seen 6 days ago Mexico I want to plor rarefaction cruves from a phyloseq object made from QIIME2 objects: otu_table = Biomtable from qiime2 Tax_table = taxonomic assign in tsv format sample_data = metadata in tsv…

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Presence of bacteria type A vs bacteria type B in different groups

Plot in R: Presence of bacteria type A vs bacteria type B in different groups 0 I would like to make a plot similar to the one here in R. I have a phyloseq object that contains the abundance of all taxa and samples associated with each group. What I…

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import phyloseq object – Iskanje Google

Piškotke in podatke uporabljamo za to: zagotavljanje in vzdrževanje Googlovih storitev; spremljanje izpadov delovanja in zaščito pred vsiljeno vsebino, prevarami in zlorabo; merjenje dejavnosti ciljnih skupin in statističnih podatkov glede spletnih mest zaradi razumevanja, kako se uporabljajo naše storitve, in izboljšanja kakovosti teh storitev. Če izberete »Sprejmi vse«, bomo piškotke…

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Query regarding Taxonomy file generation in mothur

In my experiment of 16s Data mothur generates an output where we get a taxonomy output file which I need to use for phyloseq r Bioconductor package. I want to visualize my result with this Bioconductor package phyloseq. Still, the problem I am facing is my otu based taxonomy table…

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Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem

Proctor, L. Priorities for the next 10 years of human microbiome research. Nature 569(7758), 623–625 (2019). Article  ADS  CAS  PubMed  Google Scholar  Bahl, M. I., Bergström, A. & Licht, T. R. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis….

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Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples

This prospective observational study (NCT04803695) complied with the Declaration of Helsinki (current version, Fortaleza, Brazil, October 2013). Our institution’s Internal Review Board approved the study, and all patients gave their written informed consent (No. HCB/2018/0236, Hospital Clinic Barcelona). Sputum samples and DNA extraction Thirty-three sputum samples were collected from patients…

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r – How to take random samples from a Phyloseq object

You can randomly sample from the vector of sample_names, and then prune the phyloseq object to those samples. require(“phyloseq”) # Load example data data(“GlobalPatterns”) ps <- GlobalPatterns # Sample from a physeq object with a sampling function. # ps: physeq object to be sampled # FUN: function to use for…

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query regarding visualization of data in phyloseq package

query regarding visualization of data in phyloseq package 0 @6d5973d2 Last seen 8 hours ago India I have run mothur pipeline for amplicon sequencing data. I get phyloseq object now I want to visualize various plots like an abundance of taxa, and a comparison of taxa between different samples but…

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r – Filter phyloseq sequence table using information from sample_data and tax_table

I have phyloseq object where sequence table were builded by using the function mergeSequenceTables from DADA2 package, to merge ten sequence tables from different runs. The sample_data consist of two columns 1)containing sample names same as sequence table column names and 2)study name from which samples comes from. Using this…

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ancombc documentation

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…

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Interpersonal variability of the human gut virome confounds disease signal detection in IBD

Willing, B. P. et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844–1854 (2010). Article  PubMed  Google Scholar  Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13, R79 (2012)….

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Co-diversification of an intestinal Mycoplasma and its salmonid host

Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP. Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol Evol 2016;31:689–99. Article  PubMed  Google Scholar  Groussin M, Mazel F, Alm EJ. Co-evolution and co-speciation of host-gut bacteria systems. Cell Host Microbe. 2020;28:12–22. Article  CAS  PubMed  Google Scholar  Alberdi A,…

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Metagenomic mapping of cyanobacteria and potential cyanotoxin producing taxa in large rivers of the United States

Hallegraeff, G. M. Ocean climate change, phytoplankton community responses, and harmful algal blooms: A formidable predictive challenge 1. J. Phycol. 46, 220–235 (2010). Article  CAS  Google Scholar  Itakura, S. & Imai, I. Economic impacts of harmful algal blooms on fisheries and aquaculture in western Japan—An overview of interannual variability and…

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Bioconductor – PathoStat

DOI: 10.18129/B9.bioc.PathoStat     PathoStat Statistical Microbiome Analysis Package Bioconductor version: Release (3.11) The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts,…

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Need help in applying LRT to my count abundance data

Hello all, I am little confused in using LRT of DESeq2 I have ASV count table of microbiome data on which i want to do differential abundance analysis among different groups. Here is the overview of my sample metadata So, first of all, I load the required libraries and phyloseq…

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Bioconductor – CBEA

DOI: 10.18129/B9.bioc.CBEA     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see CBEA. Competitive Balances for Taxonomic Enrichment Analysis in R Bioconductor version: 3.15 This package implements CBEA, a method to perform set-based analysis for microbiome relative abundance data. This approach constructs a…

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Metagenome reveals caprine abomasal microbiota diversity at early and late stages of Haemonchus contortus infection

All measurements and observations on animals were carried in accordance with ARRIVE guidelines and with the current law on animal experimentation and ethics, and approved by the French Ministry of Agriculture (authorization number: HC-69-2014-1) after evaluation by the Animal Care and Use Committee of French West Indies and Guyana (Comité…

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Aerial transport of bacteria by dust plumes in the Eastern Mediterranean revealed by complementary rRNA/rRNA-gene sequencing

Katra, I. et al. Richness and diversity in dust stormborne biomes at the Southeast Mediterranean. Sci. Rep. 4, 5265 (2014). Article  CAS  Google Scholar  Kellogg, C. A. & Griffin, D. W. Aerobiology and the global transport of desert dust. Trends Ecol. Evolution 21, 638–644 (2006). Article  Google Scholar  Mazar, Y.,…

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Can’t organise the sample order for Bar-plots – General

Hello everyone!We got data from 16s sequencing.I performed analysis with qiime2, then tried to use R for further analysis. So, I have created phyloseq object with next code:metadata<-read_q2metadata(“/path/metadata.tsv”, header = TRUE)features<-read_qza(“/path/table.qza”)taxonomy<-read_qza(“/path/taxonomy.qza”) taxonomy<-parse_taxonomy(taxonomy$data)head(taxonomy)phyloseq2<-qza_to_phyloseq(features = “/path/table.qza”,tree = “/path/rooted-tree.qza”,metadata = ” /path/metadata.tsv”,taxonomy = “/path/taxonomy.qza”)taxonomy = as.matrix(taxonomy) I got: phyloseqphyloseq-class experiment-level objectotu_table() OTU Table:…

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What should I do with the fastq files of negative controls? – General Discussion

I am using QIIME2 and R packages for microbiome analysis.I think QIIME2 is the best tool, especially for researchers who are about to begin the microbiome analysis. My question is about the decontamination process. I have the fastq files of 16s microbiome sequences from skin tissue samples. The sequence files…

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How to make alpha diversity boxplot?

How to make alpha diversity boxplot? 1 How to make alpha diversity boxplot? I am trying to perform alpha diversity and I performed scatter plot for shannon measure,How can I make boxplot?? meta.physeq = sample_data(meta) tax <- otu_table(tax,taxa_are_rows=FALSE) physeq.alpha = phyloseq(ASV, tax, meta.physeq) sample_data(physeq.alpha)$shannon.physeq <- estimate_richness(physeq.alpha, measures=”Shannon”) plot_richness(physeq.alpha, measures=”Shannon”) alpha_diversity…

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phyloseq – R: How can I fix an as.matrix() error message?

I am trying to create a taxonomic reference for some 16S/18S data in R and have been running into issues when following this tutorial. I am trying to create an OTU table from a taxonomy/sequence table that was bootstrapped for only 18S data. Here is the error I receive and…

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I cannot install “microbiome”

Hi there, i cannot install package “microbiome” in R (ver 4.2.1), when i input the code, it seems OK, BiocManager::install(“microbiome”, force = TRUE) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installing package(s) ‘microbiome’ trying URL…

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r – phyloseq: Discrepancies in otu counts before and after using tax_glom

Maybe I missed something in how tax_glom works but as I did not find any info here nor elsewhere on the web, maybe someone here can help. I do not provide data but I can on request. Here is the code highlighting the issue I have CYANO_gen <- CYANO %>%…

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How to pool phyloseq data?

How to pool phyloseq data? 0 @688ee615 Last seen 1 day ago United Kingdom I hope someone can help. I am trying to carry out some differential abundance analysis on some microbiome data that has come from a metabarcoding experiment using 16S illumina sequencing. I have processed my data using…

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ggplot2 – Fail to plot by group on a phyloseq object generated by R package Divnet

Once you already have your phyloseq object df_family, you can use the function estimate_richness from phyloseq. You can then join the sample meta data to this data frame of alpha diversities. Finally, you can use ggplot2 directly to customize your plot accordingly, e.g. to put different sample groups (here SampleType)…

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r – RC Bray function not accepting phyloseq otu_table as argument

I am using James Stegen et al’s code here to calculate an abundance-weighted raup-crick value for my 16S dataset. I load in my phyloseq object then extract the otu_table. I then use the otu_table as the spXsite argument in the function raup_crick_abundance(). My otu_table is available as a dput() below…

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Issues removing unwanted taxa from phyloseq object

Hi everyone, I am currently in the process of removing unwanted taxa (Kingdom=”Eukaryota”, Family=”Mitochondria”, and Order=”Chloroplast”) from a phyloseq object I created. This phyloseq object was created using my outputs from DADA2 (OTU table, taxonomy table, and metadata file). I have saved a taxonomy table in CSV format at every…

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r – How to subset (or filter?) taxa in a phyloseq object, within a grouping?

I am attempting to subset (or filter?) taxa that have relative abundance >= 35%,and belong in >= 70% of samples within a grouping (in my case it is the number of ‘clusters’ in my data). Is there a simple line of code on how to do this? I have started…

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Predict Functional potential microbial communities

Predict Functional potential microbial communities – phyloseq Silva 0 Hi, Does anyone have good tutorials/resources on how to predict the metabolic potential from microbiome data. I have preprocessed using DADA2, resulting in a phyloseq object. I assigned taxonomy with SILVA database. I found this Tax4fun package in R implemented in…

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How to order sample names with the phyloseq object for heatmap

Hello!I am new to the Rstudio!I can’t find a tutorial, or instructions for ordering our samples in the heatmapI have created the phyloseq object with the next scripts physeq<-qza_to_phyloseq(features=”file path/rarefied_table.qza”,metadata=”file path/Metadata.tsv”)taxonomy = read.csv(“file path/taxonomy.csv”,sep=”,”,row.names=1)taxonomy =as.matrix(taxonomy)TAX = tax_table(taxonomy)data_full<-merge_phyloseq(physeq,TAX) then I use ph = tax_glom(data_full, taxrank=’Genus’,NArm=FALSE)TOP = names(sort(taxa_sums(ph), TRUE)[1:20])TOPp = prune_taxa(TOP, ph)plot_heatmap(TOPp,…

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Cannot install Phyloseq and dada2

Hello all, I have been having issues installing packages that I really need to use. Basically, I cannot download either Phyloseq or dada2 and I believe it’s because I don’t have GenomeInfoDbData. But at the same time, I cannot install GenomeInfoDbData because I can’t seem to update the dependencies (“fansi”…

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combine OTU and tax table and replace actual sequences with OTU ids (Phyloseq/dada2)

This is to the part of the question “replace actual sequences with OTU ids (Phyloseq/dada2)?” I contacted the phyloseq/dada2 developers and based on Susan Holmes’ reply (github.com/joey711/phyloseq/issues/1030) I came up with this piece of code to replace the amplicon sequences with a numbered OTU header. Further discussion can be found…

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