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

Functions

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

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.