Mfuzz: Soft clustering of time series gene expression data

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

AuthorMatthias Futschik <matthias.futschik@sysbiolab.eu>
Date of publicationNone
MaintainerMatthias Futschik <matthias.futschik@sysbiolab.eu>
LicenseGPL-2
Version2.34.0
http://mfuzz.sysbiolab.eu/

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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