XYToDiffPpm             Express difference as ppm
addBeforFileExtension   Add text before file-extension
adjBy2ptReg             Linear rescaling of numeric vertor or matrix
appendNR                Append vectors or lists, without duplcating
                        common elements
arrayCV                 CV of array
asSepList               Organize data as separate list-entries
buildTree               Connect edges to from tree and extract all
                        possible branches
cbindNR                 cbind to non-redundant
checkAvSd               Check how multiple groups of data separate or
                        overlap based on mean +/- sd
checkGrpOrder           checkGrpOrder
checkGrpOrderSEM        Check order of multiple groups including
                        non-overlapping SEM-margins
checkSimValueInSer      Check for similar values in series
checkStrictOrder        Check for strict (ascencing or descending)
                        order
checkVectLength         Check length of vector
cleanReplicates         Replace most distant values by NA
closeMatchMatrix        Reorganize results of search for close
                        (similar) values in matrix-view
coinPermTest            Compare means of two vectors by permutation
                        test
colMedSds               Standard error of median for each column by
                        bootstrap
colSds                  sd for each column
colorAccording2         Transform numeric values to color-gradient
combinatIntTable        Planing for making all multiplicative
                        combinations
combineByEitherFactor   Create factor-like column regrouping data
                        regrouping simultaneaously by two factors
combineOverlapInfo      Find and combine points located very close in
                        x/y space
combineRedBasedOnCol    Combine/reduce redundant lines based on
                        specified column
combineReplFromListToMatr
                        Combine replicates from list to matrix
combineSingleT          Get all combinations with TRUE from each column
completeArrLst          Complete list of arrays for same dimensions
contribToContigPerFrag
                        Characterize individual contribution of single
                        edges in tree-structures
conv01toColNa           Convert matrix of integer to matrix of x-times
                        repeated column-names
convColorToTransp       Assign new transparency to given colors
convMatr2df             Convert matrix (eg with redundant) row-names to
                        data.frame
convToNum               Convert vector to numeric
coordOfFilt             get coordinates of values/points in matrix
                        according to filtering condition
correctToUnique         Correct vector to unique
correctWinPath          Correct mixed slash and backslash in file path
countCloseToLimits      Count from two vectors number of values close
                        within given limits
countSameStartEnd       Count same start- and end- sites of edges (or
                        fragments)
cutArrayInCluLike       Cut 3-dim array in list of matrixes (or arrays)
                        similar to organizing into clusters
cutAtMultSites          Cut character-vector at multiple sites
cutToNgrp               Cut numeric vector to n groups (ie convert to
                        factor)
diffCombin              Compute matrix of differences for all pairwise
                        combinations of numeric vector
diffPPM                 Difference in ppm between numeric values
elimCloseCoord          Eliminate close (overlapping) points (in x & y
                        space)
equLenNumber            Equal character-length number
exclExtrValues          Exclude extreme values (based on distance to
                        mean)
exponNormalize          Normalize by adjusting exponent
extr1chan               Extract just one series, ie channel, of list of
                        arrays
extrColsDeX             Flexible extraction of columns
extrNumericFromMatr     Extract numeric part of matrix or data.frame
extrSpcText             Extract specific text
extractLast2numericParts
                        Extract last two numeric parts from character
                        vector
filt3dimArr             Filter a three-dimensional array of numeric
                        data
filtSizeUniq            Filter for unique elements
filterLiColDeList       Filter lines(rows) and/or columns from all
                        suitable elements of list
filterList              Filter for unique elements
filterNetw              Filter nodes & edges for extracting networks
                        This function allows extracting and filtering
                        network-data based on fixed threshold
                        ('limInt') and add sandwich-nodes (nodes
                        inter-connecting initial nodes) out of
                        node-based queries.
findCloseMatch          Find close numeric values between two vectors
findRepeated            Find repeated elements
findSimilFrom2sets      Find similar numeric values from two
                        vectors/matrixes
findUsableGroupRange    Select groups within given range
firstLineOfDat          Filter matrix to keep only first of repeated
                        lines
firstOfRepLines         Reduce to first occurance of repeated lines
firstOfRepeated         Find first of repeated elements
fuseAnnotMatr           Fuse annotation matrix to initial matrix
fuseCommonListElem      Fuse content of list-elements with redundant
                        (duplicated) names
fusePairs               Fuse pairs to generate cluster-names
get1stOfRepeatedByCol   Get first of repeated by column
getValuesByUnique       Print matrix-content as plot
gitDataUrl              Convert ulr-name for reading in raw-mode
htmlSpecCharConv        Html special character conversion
levIndex                Transform (factor) levels into index
linModelSelect          Test multiple starting levels for linear
                        regression model, select best and plot
linRegrParamAndPVal     Fit linear regression, return parameters and
                        p-values
listBatchReplace        Replacements in list
listGroupsByNames       Organize values into list and sort by names
lmSelClu                Run lm on segmented data (from clustering)
lrbind                  rbind on lists
makeMAList              Make MA-List object
makeNRedMatr            Make non-redundant matrix
matchNamesWithReverseParts
                        Value Matching with optional reversing of
                        sub-parts of non-matching elements
matchSampToPairw        Match names to concatenated pairs of names
matr2list               Transform columns of matrix to list of vectors
mergeSelCol             Merge selected columns out of 2 matrix or
                        data.frames
mergeSelCol3            mergeSelCol3
mergeVectors            Merge Named Vectors
mergeW2                 Extended version of merge for multiple objects
                        (even without rownames)
minDiff                 Minimum distance/difference between values
moderTest2grp           Moderated pair-wise t-test from limma
moderTestXgrp           Multiple moderated pair-wise t-tests from limma
multiCharReplace        Multiple replacement of entire character
                        elements in simple vector, matrix or data.frame
multiMatch              Simple Multi-to-Multi Matching of
                        (Concatenated) Terms
nFragments              Number of fragments after cut at specific
                        character(s) within size-range
nFragments0             Number of fragments after cut at specific
                        character(s)
nNonNumChar             Count number of non-numeric characters
naOmit                  Fast na.omit
nonAmbiguousMat         Transform matrix to non-ambiguous matrix (in
                        respect to given column)
nonAmbiguousNum         make numeric vector non-ambiguous (ie unique)
nonRedundLines          Non-redundant lines of matrix
nonredDataFrame         Filter for unique elements
normalizeThis           Normalize data in various modes
numPairDeColNames       Extract pair of numeric values from vector or
                        column-names
organizeAsListOfRepl    (re)organize data of (3-dim) array as list of
                        replicates
pVal2lfdr               Convert p-values to lfdr
packageDownloadStat     Simple Package Download Statistics from CRAN
pairsAsPropensMatr      Convert pairs of node-names to non-oriented
                        propensity matrix Numerous network query tools
                        produce a listing of pairs of nodes (with one
                        pair of nodes per line).  Using this function
                        such a matrix (or data.frame) can be combined
                        to this more comprehensive view as
                        propensity-matrix.  Note, this has been
                        primarily developed for undireted interaction
                        networks, the resulting propensity-matrix does
                        not show any orientation any more.  In a number
                        of applications (eg in protein-protein
                        interaction networks, PPI) the resulting matrix
                        may be rather sparse.
partUnlist              Partial unlist of lists of lists
partialDist             Partial distance matrix (focus on closest)
pasteC                  Advanced paste-collapse
presenceFilt            Filter lines of matrix for max number of NAs
protectSpecChar         Protect Special Characters
randIndFx               Distance of categorical data (Jaccard,Rand and
                        adjusted Rand index)
rankToContigTab         Contingenty tables for fit of ranking
ratioAllComb            Calculate all ratios between x and y
ratioToPpm              Convert ratio to ppm
readCsvBatch            Read batch of csv-files
readTabulatedBatch      Batch reading of tabulated (text-) files This
                        function allows batch reading of multiple
                        tabulated text files. The files can be designed
                        specifically, alternatively all files from a
                        given directory can be read. If package
                        data.table is available, fast reading of files
                        will be performed using the function 'fread'.
readVarColumns          Read tabular content of files with variable
                        number of columns
readXlsxBatch           Read batch of Excel xlsx-files
reduceTable             Reduce table by aggregating smaller groups
regrBy1or2point         Rescaling according to reference data using
                        linear regression.
regrMultBy1or2point     Rescaling of multiple data-sets according to
                        reference data using regression
renameColumns           Rename columns
reorgByCluNo            Reorganize matrix according to
                        clustering-output
replNAbyLow             Replace NAs by low values
replPlateCV             CV of replicate plates (list of matrixes)
replicateStructure      Search and Select Groups of Replicates
rmDupl2colMatr          Remove lines of matrix redundant /duplicated
                        for 1st and 2nd column
rnormW                  Normal random number generation with close fit
                        to expected mean and sd
rowCVs                  rowCVs
rowGrpCV                row group CV
rowGrpMeans             rowMeans with destinction of groups (of
                        columns, eg groups of replicates)
rowGrpNA                Count number of NAs per row and group of
                        columns
rowGrpSds               Per line and per group sd-values
rowMedSds               sd of median for each row by bootstrap
rowSEMs                 SEM for each row
rowSds                  sd for each row (fast execution)
sampNoDeMArrayLM        Locate sample index from index or name of
                        pair-wise comparisons in list or
                        MArrayLM-object
scaleXY                 Scale data to given minimum and maxiumum
searchDataPairs         Search duplicated data over multiple columns,
                        ie pairs of data
searchLinesAtGivenSlope
                        Search points forming lines at given slope
simpleFragFig           Simple figure showing line from start- to
                        end-sites of edges (or fragments) defined by
                        their start- and end-sites 'simpleFragFig'
                        draws figure showing start- and end-sites of
                        edges (or fragments)
singleLineAnova         2-factorial Anova on single line of data
sortBy2CategorAnd1IntCol
                        Sort matrix by two categorical and one integer
                        columns
stableMode              Estimate mode (most frequent value)
standardW               Standardize (scale) data
stdErrMedBoot           Standard eror of median by boot-strap
sumNAperGroup           Count number of NAs per sub-set of columns
summarizeCols           Summarize columns (as median,mean,min,last or
                        other methods)
sysDate                 System-date (compressed format)
tTestAllVal             t.test on all individual values against all
                        other values
tableToPlot             Print matrix-content as plot
test2factLimma          2-factorial limma-style t-test
transpGraySca           Make single vector gray-gradient
treatTxtDuplicates      Locate duplicates in text and make
                        non-redundant
triCoord                Pairwise x,y combinations
trimRedundText          Trim redundant text
uniqCountReport         Report number of unique and redundant elements
                        (optional figure)
upperMaCoord            (upper) pairwise x,y combinations
withinRefRange          Check for values within range of reference
writeCsv                Write (and convert) csv files
