Mfuzz: Soft clustering of time series gene expression data
Version 2.36.0

Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)

AuthorMatthias Futschik <matthias.futschik@sysbiolab.eu>
Bioconductor views Clustering Microarray Preprocessing TimeCourse Visualization
Date of publicationNone
MaintainerMatthias Futschik <matthias.futschik@sysbiolab.eu>
LicenseGPL-2
Version2.36.0
URL http://mfuzz.sysbiolab.eu/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Mfuzz")

Popular man pages

acore: Extraction of alpha cores for soft clusters
Dmin: Calculation of minimum centroid distance for a range of...
filter.std: Filtering of genes based on their standard deviation.
kmeans2: K-means clustering for gene expression data
kmeans2.plot: Plotting results for k-means clustering
Mfuzzgui: Graphical user interface for Mfuzz package
mfuzz.plot: Plotting results for soft clustering
See all...

All man pages Function index File listing

Man pages

acore: Extraction of alpha cores for soft clusters
cselection: Repeated soft clustering for detection of empty clusters for...
Dmin: Calculation of minimum centroid distance for a range of...
fill.NA: Replacement of missing values
filter.NA: Filtering of genes based on number of non-available...
filter.std: Filtering of genes based on their standard deviation.
kmeans2: K-means clustering for gene expression data
kmeans2.plot: Plotting results for k-means clustering
membership: Calculating of membership values for new data based on...
mestimate: Estimate for optimal fuzzifier m
mfuzz: Function for soft clustering based on fuzzy c-means.
mfuzzColorBar: Plots a colour bar
Mfuzzgui: Graphical user interface for Mfuzz package
mfuzz.plot: Plotting results for soft clustering
mfuzz.plot2: Plotting results for soft clustering with additional options
overlap: Calculation of the overlap of soft clusters
overlap.plot: Visualisation of cluster overlap and global clustering...
partcoef: Calculation of the partition coefficient matrix for soft...
randomise: Randomisation of data
standardise: Standardization of expression data for clustering.
standardise2: Standardization in regards to selected time-point
table2eset: Conversion of table to Expression set object.
top.count: Determines the number for which each gene has highest...
yeast: Gene expression data of the yeast cell cycle
yeast.table: Gene expression data of the yeast cell cycle as table
yeast.table2: Gene expression data of the yeast cell cycle as table

Functions

Dmin Man page Source code
Mfuzzgui Man page Source code
acore Man page Source code
cselection Man page Source code
fill.NA Man page Source code
filter.NA Man page Source code
filter.std Man page Source code
kmeans2 Man page Source code
kmeans2.plot Man page Source code
membership Man page Source code
mestimate Man page Source code
mfuzz Man page Source code
mfuzz.plot Man page Source code
mfuzz.plot2 Man page Source code
mfuzzColorBar Man page Source code
overlap Man page Source code
overlap.plot Man page Source code
partcoef Man page Source code
randomise Man page Source code
standardise Man page Source code
standardise2 Man page Source code
table2eset Man page Source code
top.count Man page Source code
yeast Man page
yeast.table Man page
yeast.table2 Man page

Files

DESCRIPTION
NAMESPACE
R
R/Dmin.R
R/Mfuzzgui.R
R/acore.R
R/cselection.R
R/fill.NA.R
R/filter.NA.R
R/filter.std.R
R/kmeans2.R
R/kmeans2.plot.R
R/membership.R
R/mestimate.R
R/mfuzz.R
R/mfuzz.plot.R
R/mfuzz.plot2.R
R/mfuzzColorBar.R
R/overlap.R
R/overlap.plot.R
R/partcoef.R
R/randomise.R
R/standardise.R
R/standardise2.R
R/table2eset.R
R/top.count.R
build
build/vignette.rds
data
data/yeast.rda
data/yeast.table.txt
data/yeast.table2.txt
inst
inst/CITATION
inst/doc
inst/doc/Mfuzz.R
inst/doc/Mfuzz.Rnw
inst/doc/Mfuzz.pdf
man
man/Dmin.Rd
man/Mfuzzgui.Rd
man/acore.Rd
man/cselection.Rd
man/fill.NA.Rd
man/filter.NA.Rd
man/filter.std.Rd
man/kmeans2.Rd
man/kmeans2.plot.Rd
man/membership.Rd
man/mestimate.Rd
man/mfuzz.Rd
man/mfuzz.plot.Rd
man/mfuzz.plot2.Rd
man/mfuzzColorBar.Rd
man/overlap.Rd
man/overlap.plot.Rd
man/partcoef.Rd
man/randomise.Rd
man/standardise.Rd
man/standardise2.Rd
man/table2eset.Rd
man/top.count.Rd
man/yeast.Rd
man/yeast.table.Rd
man/yeast.table2.Rd
vignettes
vignettes/Mfuzz.Rnw
vignettes/MfuzzguiScreenshot.pdf
vignettes/cluster.png
vignettes/sd.png
vignettes/yeasttable3.pdf
Mfuzz documentation built on May 20, 2017, 9:19 p.m.

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