Mfuzz: Soft clustering of time series gene expression data

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

Author
Matthias Futschik <matthias.futschik@sysbiolab.eu>
Date of publication
None
Maintainer
Matthias Futschik <matthias.futschik@sysbiolab.eu>
License
GPL-2
Version
2.34.0
URLs

View on Bioconductor

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 microarray 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

Files in this package

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