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Google Keyword Rankings for : fast unifrac tutorial
1
Fast Parallel UniFrac (in R)
https://joey711.github.io/phyloseq-demo/unifrac.html
A common tool in microbial ecology studies involving many samples is to calculate the “UniFrac” distance between all pairs of samples, and then perform various ...
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https://joey711.github.io/phyloseq-demo/unifrac.html
A common tool in microbial ecology studies involving many samples is to calculate the “UniFrac” distance between all pairs of samples, and then perform various ...
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2
Fast UniFrac: facilitating high-throughput phylogenetic ...
https://www.nature.com/articles/ismej200997
A script for performing this analysis is available in the tutorial at the Fast UniFrac web site. A tree containing the same set of sequences as ...
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https://www.nature.com/articles/ismej200997
A script for performing this analysis is available in the tutorial at the Fast UniFrac web site. A tree containing the same set of sequences as ...
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3
Calculate weighted or unweighted (Fast) UniFrac distance for...
https://rdrr.io/bioc/phyloseq/man/UniFrac-methods.html
This function calculates the (Fast) UniFrac distance for all sample-pairs in a phyloseq-class object.
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https://rdrr.io/bioc/phyloseq/man/UniFrac-methods.html
This function calculates the (Fast) UniFrac distance for all sample-pairs in a phyloseq-class object.
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4
biocore/unifrac - GitHub
https://github.com/biocore/unifrac
The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac ...
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https://github.com/biocore/unifrac
The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac ...
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5
Tutorial - Ingenuity
http://pages.ingenuity.com/rs/202-RSH-885/images/build-tutorial-mam-quickguide.pdf
processing speed of the different analyses performed by the workbench, ... In the Beta analysis window select D_0.5 UniFrac but deselect ...
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http://pages.ingenuity.com/rs/202-RSH-885/images/build-tutorial-mam-quickguide.pdf
processing speed of the different analyses performed by the workbench, ... In the Beta analysis window select D_0.5 UniFrac but deselect ...
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6
Expanding the UniFrac Toolbox | PLOS ONE
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161196
The UniFrac distance metric is often used to separate groups in microbiome analysis, but requires a constant sequencing depth to work ...
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https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161196
The UniFrac distance metric is often used to separate groups in microbiome analysis, but requires a constant sequencing depth to work ...
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7
UniFrac – An online tool for comparing microbial community ...
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-371
UniFrac requires two input files: a single rooted phylogenetic tree that contains sequences derived from at least two different environmental ...
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https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-371
UniFrac requires two input files: a single rooted phylogenetic tree that contains sequences derived from at least two different environmental ...
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8
Weighted Unifrac — QIIME 2 2022.8.3 documentation
https://docs.qiime2.org/2022.8/plugins/available/diversity-lib/weighted-unifrac/
Micah Hamady, Catherine Lozupone, and Rob Knight. Fast unifrac: facilitating high-throughput phylogenetic analyses of microbial communities including ...
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https://docs.qiime2.org/2022.8/plugins/available/diversity-lib/weighted-unifrac/
Micah Hamady, Catherine Lozupone, and Rob Knight. Fast unifrac: facilitating high-throughput phylogenetic analyses of microbial communities including ...
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9
Optimizing UniFrac with OpenACC Yields Greater Than One ...
https://journals.asm.org/doi/10.1128/msystems.00028-22
As a further step, we considered the sparsity of the inputs to UniFrac. In previous algorithms of UniFrac, including Striped UniFrac and Fast UniFrac, the data ...
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https://journals.asm.org/doi/10.1128/msystems.00028-22
As a further step, we considered the sparsity of the inputs to UniFrac. In previous algorithms of UniFrac, including Striped UniFrac and Fast UniFrac, the data ...
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10
Microbiome Analysis with QIIME2: A Hands-On Tutorial
http://compbio.ucsd.edu/wp-content/uploads/2018/07/20180621_oslo_university_microbiome_analysis_with_qiime2_tutorial.pdf
For today's tutorial, we will use public data from the QIIME2 website ... unweighted UniFrac distance (a qualitative measure of community dissimilarity that.
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http://compbio.ucsd.edu/wp-content/uploads/2018/07/20180621_oslo_university_microbiome_analysis_with_qiime2_tutorial.pdf
For today's tutorial, we will use public data from the QIIME2 website ... unweighted UniFrac distance (a qualitative measure of community dissimilarity that.
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11
[PDF] Fast UniFrac: Facilitating high-throughput phylogenetic ...
https://www.semanticscholar.org/paper/Fast-UniFrac%3A-Facilitating-high-throughput-analyses-Hamady-Lozupone/ac9f04999666b73eba7eea627f65b9ee10fff163
The potential of Fast UniFrac is shown using examples from three data types: Sanger-sequencing studies of diverse free-living and ...
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https://www.semanticscholar.org/paper/Fast-UniFrac%3A-Facilitating-high-throughput-analyses-Hamady-Lozupone/ac9f04999666b73eba7eea627f65b9ee10fff163
The potential of Fast UniFrac is shown using examples from three data types: Sanger-sequencing studies of diverse free-living and ...
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12
Unifrac and Tree Roots - John Quensen
https://john-quensen.com/r/unifrac-and-tree-roots/
Both methods calculate unrooted trees, and calculation of Unifrac distances ... Phyloseq assigns a root randomly, which is certainly fast, ...
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https://john-quensen.com/r/unifrac-and-tree-roots/
Both methods calculate unrooted trees, and calculation of Unifrac distances ... Phyloseq assigns a root randomly, which is certainly fast, ...
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13
phyloseq.pdf - Bioconductor
https://www.bioconductor.org/packages/devel/bioc/manuals/phyloseq/man/phyloseq.pdf
Depending on the method argument, distance() wraps one of UniFrac, ... serial import will be just as fast and the import is often only ...
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https://www.bioconductor.org/packages/devel/bioc/manuals/phyloseq/man/phyloseq.pdf
Depending on the method argument, distance() wraps one of UniFrac, ... serial import will be just as fast and the import is often only ...
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14
454 Overview Tutorial: de novo OTU picking and ... - QIIME
http://qiime.org/tutorials/tutorial.html
To make this tutorial run quickly on a personal computer, we will use a subset of the data ... and is necessary for UniFrac diversity measurements and other ...
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http://qiime.org/tutorials/tutorial.html
To make this tutorial run quickly on a personal computer, we will use a subset of the data ... and is necessary for UniFrac diversity measurements and other ...
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15
Microbiome tutorial with QIIME 2 - F1000Research
https://f1000research.com/documents/10-798/pdf
This course will guide you through microbiome data analysis in a practical way ... commands will run fast. ... weighted-unifrac-life-stage-significance.qzv.
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https://f1000research.com/documents/10-798/pdf
This course will guide you through microbiome data analysis in a practical way ... commands will run fast. ... weighted-unifrac-life-stage-significance.qzv.
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16
skbio.diversity.beta.unweighted_unifrac
http://scikit-bio.org/docs/0.4.2/generated/generated/skbio.diversity.beta.unweighted_unifrac.html
If computing unweighted UniFrac for multiple pairs of samples, using skbio.diversity.beta_diversity will be much faster than calling this function ...
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http://scikit-bio.org/docs/0.4.2/generated/generated/skbio.diversity.beta.unweighted_unifrac.html
If computing unweighted UniFrac for multiple pairs of samples, using skbio.diversity.beta_diversity will be much faster than calling this function ...
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17
UniFrac metric - drive5
https://drive5.com/usearch/manual/unifrac.html
Video talks on 16S data analysis posted. URMAP ultra-fast read mapper posted (paper). ~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).
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https://drive5.com/usearch/manual/unifrac.html
Video talks on 16S data analysis posted. URMAP ultra-fast read mapper posted (paper). ~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).
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18
Vignette for phyloseq: Analysis of high ... - Bioconductor
https://bioconductor.riken.jp/packages/3.1/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html
See the microbio_me_qiime tutorial for more details and examples downloading and importing into ... See the phyloseq demo page about fast parallel UniFrac.
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https://bioconductor.riken.jp/packages/3.1/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html
See the microbio_me_qiime tutorial for more details and examples downloading and importing into ... See the phyloseq demo page about fast parallel UniFrac.
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19
October 2013 Galaxy Update
https://galaxyproject.org/galaxy-updates/2013-10
See "Fast UniFrac: facilitating high-throughput phylogenetic analyses of ... A tutorial on using the web server and a Galaxy Tool Shed repository are also ...
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https://galaxyproject.org/galaxy-updates/2013-10
See "Fast UniFrac: facilitating high-throughput phylogenetic analyses of ... A tutorial on using the web server and a Galaxy Tool Shed repository are also ...
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20
Using Trees in Microbiome Analysis
https://si.biostat.washington.edu/sites/default/files/modules/2018-SISMID-04.pdf
Tree-Building (“quick” overview) ... UniFrac and variants ... MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
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https://si.biostat.washington.edu/sites/default/files/modules/2018-SISMID-04.pdf
Tree-Building (“quick” overview) ... UniFrac and variants ... MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
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21
Tutorial for microbiome analysis in R - Yan Hui
https://www.yanh.org/2021/01/01/microbiome-r/
This tutorial cover the common microbiome analysis e.g. alpha/beta ... Besides, the UniFrac distance calculation by phyloseq has not been ...
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https://www.yanh.org/2021/01/01/microbiome-r/
This tutorial cover the common microbiome analysis e.g. alpha/beta ... Besides, the UniFrac distance calculation by phyloseq has not been ...
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22
Vignette for phyloseq: Analysis of high-throughput microbiome ...
https://bioc.ism.ac.jp/packages/3.7/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html
If you find phyloseq and/or its tutorials useful, ... A quick way to load it is: ... It also supports the Fast UniFrac distance function ...
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https://bioc.ism.ac.jp/packages/3.7/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html
If you find phyloseq and/or its tutorials useful, ... A quick way to load it is: ... It also supports the Fast UniFrac distance function ...
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23
A guide to human microbiome research: study design, sample ...
https://journals.lww.com/cmj/Fulltext/2020/08050/A_guide_to_human_microbiome_research__study.10.aspx
The UniFrac distance, which can be unweighted or weighted, estimates differences between samples or groups based on phylogenetic distance.
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https://journals.lww.com/cmj/Fulltext/2020/08050/A_guide_to_human_microbiome_research__study.10.aspx
The UniFrac distance, which can be unweighted or weighted, estimates differences between samples or groups based on phylogenetic distance.
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24
MiSeq SOP - Mothur
https://mothur.org/wiki/miseq_sop/
We were curious whether the rapid change in weight observed during the first 10 dpw ... For this tutorial you will need mothur and several sets of files:.
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https://mothur.org/wiki/miseq_sop/
We were curious whether the rapid change in weight observed during the first 10 dpw ... For this tutorial you will need mothur and several sets of files:.
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25
biocontainers/unifrac - Quay.io
https://quay.io/repository/biocontainers/unifrac?tab=tags
› repository › biocontainers › unifrac
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https://quay.io/repository/biocontainers/unifrac?tab=tags
› repository › biocontainers › unifrac
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26
Phylogenetic placement of exact amplicon sequences ...
https://digitalcommons.wustl.edu/cgi/viewcontent.cgi?article=7912&context=open_access_pubs
processed significantly faster as placements for the majority of affected sOTUs ... coordinate analysis (PCoA) of unweighted UniFrac distances showed major ...
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https://digitalcommons.wustl.edu/cgi/viewcontent.cgi?article=7912&context=open_access_pubs
processed significantly faster as placements for the majority of affected sOTUs ... coordinate analysis (PCoA) of unweighted UniFrac distances showed major ...
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27
Tutorial: Assessing metagenomics software with the ... - bioRxiv
http://biorxiv.org/cgi/reprint/2020.08.11.245712v1
In this tutorial, we describe emerging standards in ... abundance metrics such as UniFrac, L1 norm and the Bray-Curtis distance. Bioboxes33.
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http://biorxiv.org/cgi/reprint/2020.08.11.245712v1
In this tutorial, we describe emerging standards in ... abundance metrics such as UniFrac, L1 norm and the Bray-Curtis distance. Bioboxes33.
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28
Forensic identification using skin bacterial communities - PNAS
https://www.pnas.org/doi/10.1073/pnas.1000162107
The UniFrac algorithm uses the degree of phylogenetic overlap between any pair ... horizontally at maximum speed for 2 min using the MO BIO vortex adapter.
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https://www.pnas.org/doi/10.1073/pnas.1000162107
The UniFrac algorithm uses the degree of phylogenetic overlap between any pair ... horizontally at maximum speed for 2 min using the MO BIO vortex adapter.
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29
microbiomeSeq: An R package for microbial community ...
https://userweb.eng.gla.ac.uk/umer.ijaz/projects/microbiomeSeq_Tutorial.html
Here we present a tutorial with minimum working examples to demonstrate ... “wunifrac”and “unifrac”. grouping_column is a character string ...
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https://userweb.eng.gla.ac.uk/umer.ijaz/projects/microbiomeSeq_Tutorial.html
Here we present a tutorial with minimum working examples to demonstrate ... “wunifrac”and “unifrac”. grouping_column is a character string ...
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30
OTU Clustering Step by Step - Tutorial
https://resources.qiagenbioinformatics.com/tutorials/OTU_Clustering_Steps.pdf
Hence, the phylogenetic tree used for calculating the phylogenetic diversity and the UniFrac distances disregards the low abundance OTUs by ...
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https://resources.qiagenbioinformatics.com/tutorials/OTU_Clustering_Steps.pdf
Hence, the phylogenetic tree used for calculating the phylogenetic diversity and the UniFrac distances disregards the low abundance OTUs by ...
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31
MICROBIOME DATA & ANALYSIS
http://evomics.org/wp-content/uploads/2019/01/evomics-low-res.pdf
Anvi'o: helps with manual refinement. (More later) ... Can map reads to genomes (often not faster than assembly; high FP) ... e.g., UniFrac, Bray-Curtis.
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http://evomics.org/wp-content/uploads/2019/01/evomics-low-res.pdf
Anvi'o: helps with manual refinement. (More later) ... Can map reads to genomes (often not faster than assembly; high FP) ... e.g., UniFrac, Bray-Curtis.
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32
Qiime2 - Metagenomics - Bioinformatics Workbook
https://bioinformaticsworkbook.org/dataAnalysis/Metagenomics/Qiime2.html
By Adam Rivers, Designed from the official QIIME2 tutorials ... and subsampling each sample down to 10,000 reads to speed up analysis during this tutorial.
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https://bioinformaticsworkbook.org/dataAnalysis/Metagenomics/Qiime2.html
By Adam Rivers, Designed from the official QIIME2 tutorials ... and subsampling each sample down to 10,000 reads to speed up analysis during this tutorial.
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33
DNA Subway - CyVerse Learning Home
https://learning.cyverse.org/dna_subway_guide/
Summary: Together, Kallisto and Sleuth are quick, powerful ways to analyze RNA-Seq data. Walkthrough of DNA Subway Purple Line (beta testing documentation)¶.
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https://learning.cyverse.org/dna_subway_guide/
Summary: Together, Kallisto and Sleuth are quick, powerful ways to analyze RNA-Seq data. Walkthrough of DNA Subway Purple Line (beta testing documentation)¶.
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34
Effects on Soil Enzyme Activity and Microbial Community ...
https://pubs.acs.org/doi/10.1021/acs.est.1c01084
Fast UniFrac overcomes these issues, allowing integration of larger nos. of sequences and samples into a single anal. Its new array-based ...
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https://pubs.acs.org/doi/10.1021/acs.est.1c01084
Fast UniFrac overcomes these issues, allowing integration of larger nos. of sequences and samples into a single anal. Its new array-based ...
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35
Bioinformatics III: qiime2 - HackMD
https://hackmd.io/@MAE-MBL/HylpoaOF5
Create a tree; Weighted and unweighted unifrac. Visualizing Beta Diversity in PCo ... Here is a link to the MAE Unix tutorial if you need a quick review.
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https://hackmd.io/@MAE-MBL/HylpoaOF5
Create a tree; Weighted and unweighted unifrac. Visualizing Beta Diversity in PCo ... Here is a link to the MAE Unix tutorial if you need a quick review.
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36
Best practices for analyzing microbiomes
https://repository.library.noaa.gov/view/noaa/28862/noaa_28862_DS1.pdf
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and. PhyloChip data. ISME J. 4, ...
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https://repository.library.noaa.gov/view/noaa/28862/noaa_28862_DS1.pdf
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and. PhyloChip data. ISME J. 4, ...
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37
GENEWIZ MetaVx™ 2.0 Report
https://web.genewiz.com/hubfs/Case%20Studies/MetaVx/MetaVx_Example_Report.pdf
Software: QIIME v1.7 (http://QIIME.org/tutorials/otu picking.html) ... Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial.
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https://web.genewiz.com/hubfs/Case%20Studies/MetaVx/MetaVx_Example_Report.pdf
Software: QIIME v1.7 (http://QIIME.org/tutorials/otu picking.html) ... Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial.
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38
Microbial community analysis with QIIME2
https://genomeintelligence.org/?p=1443
QIIME2 is on the cluster but you can also do this tutorial on a laptop. ... (takes about 9 hrs) and do the rest of the fast steps locally.
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https://genomeintelligence.org/?p=1443
QIIME2 is on the cluster but you can also do this tutorial on a laptop. ... (takes about 9 hrs) and do the rest of the fast steps locally.
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39
F. Compare Samples to Each Other - Werner Lab
http://www.wernerlab.org/teaching/qiime/overview/f
If you have many samples (in this tutorial we have nine samples), ... distances between samples were calculated using unweighted UniFrac, ...
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http://www.wernerlab.org/teaching/qiime/overview/f
If you have many samples (in this tutorial we have nine samples), ... distances between samples were calculated using unweighted UniFrac, ...
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40
phyloseq: Reproducible interactive analysis of microbiome ...
https://www.r-bloggers.com/2012/04/phyloseq-reproducible-interactive-analysis-of-microbiome-census-data-using-r/
R news and tutorials contributed by hundreds of R bloggers ... optionally-parallel implementation of Fast UniFrac (weighted and unweighted), ...
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https://www.r-bloggers.com/2012/04/phyloseq-reproducible-interactive-analysis-of-microbiome-census-data-using-r/
R news and tutorials contributed by hundreds of R bloggers ... optionally-parallel implementation of Fast UniFrac (weighted and unweighted), ...
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41
Data analysis for 16S microbial profiling from different ...
https://www.sciencedirect.com/science/article/pii/S0167701214002528
Procrustes plot comparing principal coordinates of unweighted UniFrac ... the analysis workflow on UPARSE is faster than on QIIME (data not shown).
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https://www.sciencedirect.com/science/article/pii/S0167701214002528
Procrustes plot comparing principal coordinates of unweighted UniFrac ... the analysis workflow on UPARSE is faster than on QIIME (data not shown).
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42
Photoautotrophic symbiont and geography are major factors ...
https://www.academia.edu/80749850/Photoautotrophic_symbiont_and_geography_are_major_factors_affecting_highly_structured_and_diverse_bacterial_communities_in_the_lichen_microbiome?f_ri=1444
Based on the DNA concentration, run, in accordance with the Fast UniFrac tutorial (http:// as determined by using a Qubit fluorometer (Invitrogen), ...
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https://www.academia.edu/80749850/Photoautotrophic_symbiont_and_geography_are_major_factors_affecting_highly_structured_and_diverse_bacterial_communities_in_the_lichen_microbiome?f_ri=1444
Based on the DNA concentration, run, in accordance with the Fast UniFrac tutorial (http:// as determined by using a Qubit fluorometer (Invitrogen), ...
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43
pplacer - Matsen Group
https://matsen.fhcrc.org/pplacer/
Pplacer is designed to be fast, to give useful information about uncertainty, ... There is also the fairly self-explanatory guppy unifrac and guppy rarefy ...
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https://matsen.fhcrc.org/pplacer/
Pplacer is designed to be fast, to give useful information about uncertainty, ... There is also the fairly self-explanatory guppy unifrac and guppy rarefy ...
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44
Operate in the Unix Environment Objectives - QUBES Hub
https://qubeshub.org/publications/731/serve/2/5462?el=1&download=1
Single read runs are faster and cheaper but contain more errors. ... Create a new directory “qiime2-moving-pictures-tutorial” and change to that directory ...
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https://qubeshub.org/publications/731/serve/2/5462?el=1&download=1
Single read runs are faster and cheaper but contain more errors. ... Create a new directory “qiime2-moving-pictures-tutorial” and change to that directory ...
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45
Tutorial: assessing metagenomics software with ... - NSF PAR
https://par.nsf.gov/servlets/purl/10247246
In this tutorial, we describe emerging standards in computational meta- ... purity, F1 score, Jaccard index) and abundance metrics such as UniFrac, ...
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https://par.nsf.gov/servlets/purl/10247246
In this tutorial, we describe emerging standards in computational meta- ... purity, F1 score, Jaccard index) and abundance metrics such as UniFrac, ...
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46
UniFrac - Wikipedia
https://en.wikipedia.org/wiki/UniFrac
UniFrac is a distance metric used for comparing biological communities. It differs from dissimilarity measures such as Bray-Curtis dissimilarity in that it ...
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https://en.wikipedia.org/wiki/UniFrac
UniFrac is a distance metric used for comparing biological communities. It differs from dissimilarity measures such as Bray-Curtis dissimilarity in that it ...
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47
Microbiome 101
https://sites.unimi.it/dmora/materiali/ANU2012/BioInfoTools.pdf
Alpha diversity rarefacwon QIIME tutorial and some examples ... Raw unweighted Unifrac: sum of branch length that is ... four Fast samples are all blue.
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https://sites.unimi.it/dmora/materiali/ANU2012/BioInfoTools.pdf
Alpha diversity rarefacwon QIIME tutorial and some examples ... Raw unweighted Unifrac: sum of branch length that is ... four Fast samples are all blue.
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48
Microbiota Procesing in mothur: standard operating procedure ...
https://rpubs.com/dillmcfarlan/mothurSOP
This will be faster and prevent typos. ... The goal of this tutorial is to demonstrate standard operating procedures (SOP) for processing ...
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https://rpubs.com/dillmcfarlan/mothurSOP
This will be faster and prevent typos. ... The goal of this tutorial is to demonstrate standard operating procedures (SOP) for processing ...
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49
Using MicrobiomeAnalyst for comprehensive statistical ...
https://edisciplinas.usp.br/pluginfile.php/5269697/mod_resource/content/2/2020-Using%20MicrobiomeAnalyst%20for%20comprehensive%20statistical%2C%20functional%2C%20and%20meta-analysis%20of%20microbiome%20data.pdf
Rapid advances in high-throughput sequencing technologies have profoundly changed the study ... would like to perform phylogenetic tree analysis or UniFrac ...
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https://edisciplinas.usp.br/pluginfile.php/5269697/mod_resource/content/2/2020-Using%20MicrobiomeAnalyst%20for%20comprehensive%20statistical%2C%20functional%2C%20and%20meta-analysis%20of%20microbiome%20data.pdf
Rapid advances in high-throughput sequencing technologies have profoundly changed the study ... would like to perform phylogenetic tree analysis or UniFrac ...
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50
Root-Associated Endophytic Bacterial Community ... - MDPI
https://www.mdpi.com/2076-2607/7/2/47/htm
Due to high crude protein and sugar contents, fast growth, a strong tillering ... The results of the PCoA based on unweighted Unifrac distances demonstrated ...
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https://www.mdpi.com/2076-2607/7/2/47/htm
Due to high crude protein and sugar contents, fast growth, a strong tillering ... The results of the PCoA based on unweighted Unifrac distances demonstrated ...
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51
Microbial community structure of hydrothermal deposits from ...
https://fire.biol.wwu.edu/cmoyer/zztemp_fire/biol508_F12/Flores_454_%20MAR%20vents_em11.pdf
the bacterial weighted UniFrac distances. ... Manual classifications using ARB ... Fast UniFrac pipeline was used for the subsequent analysis,.
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https://fire.biol.wwu.edu/cmoyer/zztemp_fire/biol508_F12/Flores_454_%20MAR%20vents_em11.pdf
the bacterial weighted UniFrac distances. ... Manual classifications using ARB ... Fast UniFrac pipeline was used for the subsequent analysis,.
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52
Evaluating the accuracy of amplicon-based microbiome ...
https://d-nb.info/1135808856/34
were more robust against errors introduced in processing than Weighted UniFrac. The settings suggested in the tutorials were among the worst performing in ...
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https://d-nb.info/1135808856/34
were more robust against errors introduced in processing than Weighted UniFrac. The settings suggested in the tutorials were among the worst performing in ...
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53
Introducing mothur - The Schloss Lab
https://www.schlosslab.org/assets/pdf/2009_schloss_a.pdf
(23), LIBSHUFF (25, 26), UniFrac (11, 12), AMOVA and ... the ability to more quickly address bugs, incorporate user sug-.
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https://www.schlosslab.org/assets/pdf/2009_schloss_a.pdf
(23), LIBSHUFF (25, 26), UniFrac (11, 12), AMOVA and ... the ability to more quickly address bugs, incorporate user sug-.
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54
The Microbial Phyllogeography of the Carnivorous Plant ... - jstor
https://www.jstor.org/stable/41489099
distance matrix prepared in Fast UniFrac). Ten thousand permutations were ... Clarke KR, Gorley RN (2006) PRIMER v6: user manual/tutorial.
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https://www.jstor.org/stable/41489099
distance matrix prepared in Fast UniFrac). Ten thousand permutations were ... Clarke KR, Gorley RN (2006) PRIMER v6: user manual/tutorial.
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55
Spatial structuring of bacterial communities within individual ...
https://www.fiererlab.org/s/Leff_etal_2015_EnvMicro_published.pdf
This ordination was created from unweighted UniFrac distances. Bacterial biogeography within individual trees 2355. © 2014 Society for Applied Microbiology and ...
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https://www.fiererlab.org/s/Leff_etal_2015_EnvMicro_published.pdf
This ordination was created from unweighted UniFrac distances. Bacterial biogeography within individual trees 2355. © 2014 Society for Applied Microbiology and ...
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56
guide_to_amplicon_sequencing...
https://wiki.qcbs.ca/guide_to_amplicon_sequencing_experiment
From Soil to Sequence Submission - A guide to amplicon sequencing experiments ... Fast UniFrac An interesting and widely used platform for ...
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https://wiki.qcbs.ca/guide_to_amplicon_sequencing_experiment
From Soil to Sequence Submission - A guide to amplicon sequencing experiments ... Fast UniFrac An interesting and widely used platform for ...
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57
Part 2: CLC Microbial Genomics Module
https://digitalinsights.qiagen.com/news/blog/discovery/microbial-genomics-module-part-2-new-visualizations-for-diversity-analysis/
... several different metrics for estimating the beta diversity in a set of samples, including Bray-Curtis, Jaccard, Euclidean, and UniFrac.
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https://digitalinsights.qiagen.com/news/blog/discovery/microbial-genomics-module-part-2-new-visualizations-for-diversity-analysis/
... several different metrics for estimating the beta diversity in a set of samples, including Bray-Curtis, Jaccard, Euclidean, and UniFrac.
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58
Galaxy | Deng Lab
http://mem.rcees.ac.cn:8080/
2021-12-24 Striped Unifrac is ready now. ... 2019-7-26 "Fast expectation-maximization for microbialsource tracking (FEAST)" is online now!
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http://mem.rcees.ac.cn:8080/
2021-12-24 Striped Unifrac is ready now. ... 2019-7-26 "Fast expectation-maximization for microbialsource tracking (FEAST)" is online now!
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59
Phylogenetics and the Human Microbiome | Systematic Biology
https://academic.oup.com/sysbio/article/64/1/e26/2847641
They are generally variants of the “UniFrac” phylogenetic dissimilarity measure ... In general, human microbiome researchers are interested in quickly doing ...
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https://academic.oup.com/sysbio/article/64/1/e26/2847641
They are generally variants of the “UniFrac” phylogenetic dissimilarity measure ... In general, human microbiome researchers are interested in quickly doing ...
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60
here - Melbourne Bioinformatics
https://www.melbournebioinformatics.org.au/tutorials/tutorials/qiime2/media/QIIME2_workshop_AustraliaBiocommons_220222.pdf
other QIIME2 tutorials) ... --p-n-threads 0 \ #number of cores; 0 = all cores used = faster ... #some analyses (i.e. unifrac).
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https://www.melbournebioinformatics.org.au/tutorials/tutorials/qiime2/media/QIIME2_workshop_AustraliaBiocommons_220222.pdf
other QIIME2 tutorials) ... --p-n-threads 0 \ #number of cores; 0 = all cores used = faster ... #some analyses (i.e. unifrac).
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61
A Unweighted And B Weighted Unifrac Measures Of Beta
https://www.otosection.com/a-unweighted-and-b-weighted-unifrac-measures-of-beta/
If computing weighted unifrac for multiple pairs of samples, using skbio.diversity.beta diversity will be much faster than calling this function ...
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https://www.otosection.com/a-unweighted-and-b-weighted-unifrac-measures-of-beta/
If computing weighted unifrac for multiple pairs of samples, using skbio.diversity.beta diversity will be much faster than calling this function ...
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62
R package for Unifrac and Weighted Unifrac other ... - BioStars
https://www.biostars.org/p/387467/
To help with the latter I gave you the link to the phyloseq tutorial part on how to convert various R data structures into phyloseq objects. ADD ...
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https://www.biostars.org/p/387467/
To help with the latter I gave you the link to the phyloseq tutorial part on how to convert various R data structures into phyloseq objects. ADD ...
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63
UniFrac in R
https://starletbeauty.shop/en/unifrac-in-r.html
Fast UniFrac tutorial Introduction This tutorial takes you through the steps of analyzing data in the Fast UniFrac web application.
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https://starletbeauty.shop/en/unifrac-in-r.html
Fast UniFrac tutorial Introduction This tutorial takes you through the steps of analyzing data in the Fast UniFrac web application.
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64
Research on Nitrification and Related Processes, Part B
https://books.google.com/books?id=U0jWfcp_bkYC&pg=PA47&lpg=PA47&dq=fast+unifrac+tutorial&source=bl&ots=vi32L07Fgr&sig=ACfU3U3UeNKxAcg0gFovNplJUm1U396l2Q&hl=en&sa=X&ved=2ahUKEwj5heaU-9v7AhU-hXIEHafjBQYQ6AF6BQiUAhAD
With its expansion to a new version of Fast UniFrac (Hamady et al., 2010), more features and computing power were added to this valuable statistical tool.
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https://books.google.com/books?id=U0jWfcp_bkYC&pg=PA47&lpg=PA47&dq=fast+unifrac+tutorial&source=bl&ots=vi32L07Fgr&sig=ACfU3U3UeNKxAcg0gFovNplJUm1U396l2Q&hl=en&sa=X&ved=2ahUKEwj5heaU-9v7AhU-hXIEHafjBQYQ6AF6BQiUAhAD
With its expansion to a new version of Fast UniFrac (Hamady et al., 2010), more features and computing power were added to this valuable statistical tool.
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65
Microbiome r package tutorial - Pressure Applied Customs
https://zzo.pressureappliedcustoms.info/microbiome-r-package-tutorial.html
Native R/C, parallelized implementation of UniFrac distance calculations. ... goal of developing this package is to help users analyse microbiome data fast.
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https://zzo.pressureappliedcustoms.info/microbiome-r-package-tutorial.html
Native R/C, parallelized implementation of UniFrac distance calculations. ... goal of developing this package is to help users analyse microbiome data fast.
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66
phyloseq heatmap r - Dogana d'Acqua Rooms & Art - livorno
https://bblivornodoganadacqua.it/phyloseq-heatmap-r.html
An unweighted UniFrac distance matrix only considers the presence/absence of ... I have gone through the phyloseq tutorial but still confused as I have no ...
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https://bblivornodoganadacqua.it/phyloseq-heatmap-r.html
An unweighted UniFrac distance matrix only considers the presence/absence of ... I have gone through the phyloseq tutorial but still confused as I have no ...
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67
Microbiome Sample Comparison and Search: From Pair-Wise ...
https://www.frontiersin.org/articles/10.3389/fmicb.2021.642439/full
Thus, these two approaches are suitable for a quick comparison of samples in ... The UniFrac, Fast UniFrac, and Striped UniFrac methods are ...
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https://www.frontiersin.org/articles/10.3389/fmicb.2021.642439/full
Thus, these two approaches are suitable for a quick comparison of samples in ... The UniFrac, Fast UniFrac, and Striped UniFrac methods are ...
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68
Analysis of Closed Reference Process — Qiita-GNPS ...
https://cmi-workshop.readthedocs.io/en/latest/qiita-16S-analysis.html
The final alpha diversity analysis in this tutorial uses Faith's phylogenetic ... To perform unweighted UniFrac analysis, select the “rarefied table (BIOM)” ...
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https://cmi-workshop.readthedocs.io/en/latest/qiita-16S-analysis.html
The final alpha diversity analysis in this tutorial uses Faith's phylogenetic ... To perform unweighted UniFrac analysis, select the “rarefied table (BIOM)” ...
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