GUniFrac (Q21987): Difference between revisions

← Older edit

@@ Property / last update @@
-October 2022Timestamp +2022-10-23T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2022-10-23T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / last update: 23 October 2022 / rank @@
-Normal rank
@@ Property / imports @@
-ggrepel
@@ Property / imports: ggrepel / rank @@
-Normal rank
@@ Property / imports @@
-foreach
@@ Property / imports: foreach / rank @@
-Normal rank
@@ Property / imports @@
-modeest
@@ Property / imports: modeest / rank @@
-Normal rank
@@ Property / software version identifier @@
+.0
@@ Property / software version identifier: 1.0 / rank @@
+Normal rank
@@ Property / software version identifier: 1.0 / qualifier @@
+publication date: 28 April 2012Timestamp +2012-04-28T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2012-04-28T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.1
@@ Property / software version identifier: 1.1 / rank @@
+Normal rank
@@ Property / software version identifier: 1.1 / qualifier @@
+publication date: 13 February 2018Timestamp +2018-02-13T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2018-02-13T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.2
@@ Property / software version identifier: 1.2 / rank @@
+Normal rank
@@ Property / software version identifier: 1.2 / qualifier @@
+publication date: 3 May 2021Timestamp +2021-05-03T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2021-05-03T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.3
@@ Property / software version identifier: 1.3 / rank @@
+Normal rank
@@ Property / software version identifier: 1.3 / qualifier @@
+publication date: 18 August 2021Timestamp +2021-08-18T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2021-08-18T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.4
@@ Property / software version identifier: 1.4 / rank @@
+Normal rank
@@ Property / software version identifier: 1.4 / qualifier @@
+publication date: 10 November 2021Timestamp +2021-11-10T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2021-11-10T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.5
@@ Property / software version identifier: 1.5 / rank @@
+Normal rank
@@ Property / software version identifier: 1.5 / qualifier @@
+publication date: 6 April 2022Timestamp +2022-04-06T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2022-04-06T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.6
@@ Property / software version identifier: 1.6 / rank @@
+Normal rank
@@ Property / software version identifier: 1.6 / qualifier @@
+publication date: 17 May 2022Timestamp +2022-05-17T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2022-05-17T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.8
@@ Property / software version identifier: 1.8 / rank @@
+Normal rank
@@ Property / software version identifier: 1.8 / qualifier @@
+publication date: 14 September 2023Timestamp +2023-09-14T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2023-09-14T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / last update @@
+September 2023Timestamp +2023-09-14T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2023-09-14T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / last update: 14 September 2023 / rank @@
+Normal rank
@@ Property / description @@
+A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances,  Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and  (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.
+Normal rank
@@ Property / author @@
+Jun Chen
@@ Property / author: Jun Chen / rank @@
+Normal rank
@@ Property / copyright license @@
+GNU General Public License, version 3.0
@@ Property / copyright license: GNU General Public License, version 3.0 / rank @@
+Normal rank
@@ Property / imports @@
+Rcpp
@@ Property / imports: Rcpp / rank @@
+Normal rank
@@ Property / imports: Rcpp / qualifier @@
+software version identifier: ≥ 0.12.13
@@ Property / imports @@
+vegan
@@ Property / imports: vegan / rank @@
+Normal rank
@@ Property / imports @@
+ggplot2
@@ Property / imports: ggplot2 / rank @@
+Normal rank
@@ Property / imports @@
+matrixStats
@@ Property / imports: matrixStats / rank @@
+Normal rank
@@ Property / imports @@
+Matrix
@@ Property / imports: Matrix / rank @@
+Normal rank
@@ Property / imports @@
+ape
@@ Property / imports: ape / rank @@
+Normal rank
@@ Property / imports @@
+parallel
@@ Property / imports: parallel / rank @@
+Normal rank
@@ Property / imports @@
+stats
@@ Property / imports: stats / rank @@
+Normal rank
@@ Property / imports @@
+utils
@@ Property / imports: utils / rank @@
+Normal rank
@@ Property / imports @@
+statmod
@@ Property / imports: statmod / rank @@
+Normal rank
@@ Property / imports @@
+rmutil
@@ Property / imports: rmutil / rank @@
+Normal rank
@@ Property / imports @@
+dirmult
@@ Property / imports: dirmult / rank @@
+Normal rank
@@ Property / imports @@
+MASS
@@ Property / imports: MASS / rank @@
+Normal rank
@@ Property / imports @@
+ggrepel
@@ Property / imports: ggrepel / rank @@
+Normal rank
@@ Property / imports @@
+foreach
@@ Property / imports: foreach / rank @@
+Normal rank
@@ Property / imports @@
+modeest
@@ Property / imports: modeest / rank @@
+Normal rank
@@ Property / imports @@
+inline
@@ Property / imports: inline / rank @@
+Normal rank
@@ Property / imports @@
+methods
@@ Property / imports: methods / rank @@
+Normal rank
@@ Property / depends on software @@
+R
@@ Property / depends on software: R / rank @@
+Normal rank
@@ Property / depends on software: R / qualifier @@
+software version identifier: ≥ 3.5.0
@@ Property / source code repository @@
+https://github.com/cran/GUniFrac
@@ Property / source code repository: https://github.com/cran/GUniFrac / rank @@
+Normal rank
@@ Property / Software Heritage ID @@
+swh:1:snp:aaaab092d7525968d0ca8c38f305a2ff1e9ec99f
+Normal rank
+source code repository: https://github.com/cran/GUniFrac
+point in time: 16 October 2023Timestamp +2023-10-16T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2023-10-16T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ links / mardi / name / links / mardi / name @@
+Software:21987

Latest revision as of 16:30, 21 March 2024

Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis

Language	Label	Description	Also known as
English	GUniFrac	Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis

Statements

0 references

0 references

software version identifier

1.7

publication date

23 October 2022

0 references

1.0

publication date

28 April 2012

0 references

1.1

publication date

13 February 2018

0 references

1.2

publication date

3 May 2021

0 references

1.3

publication date

18 August 2021

0 references

1.4

publication date

10 November 2021

0 references

1.5

publication date

6 April 2022

0 references

1.6

publication date

17 May 2022

0 references

1.8

publication date

14 September 2023

0 references

0 references

0 references

0 references

MaRDI software profile

0 references

last update

14 September 2023

0 references

description

A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.

0 references

author

Jun Chen

0 references

copyright license

GNU General Public License, version 3.0

0 references

imports

Rcpp

software version identifier

≥ 0.12.13

0 references